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GraphPad Prism User Guide

1. ccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeaeeeeeeeeeaaeeeeeeenes 386 4 Exporting for publishing in journals ccccccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeesaeeeeeesaeeeeeesaeeeeeseaneeeees 389 5 RGB vs CMYK color MOdeIS 0ccccceeeeeeeeeee ee eeeeeeeeeeeeee ee eeeeee ee eeeeeeeeeeseeeeeeeseeeeeeeeeeneeesenenes 391 6 Fonts and EPS file sis ciiccccciccciiccctecvceceteeieccceeevec chteeide ccteeees ceteedessctevens eateries ANENA aE KANAN kaaa 392 7 The size of exported graphs and layOut cccececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseneees 393 8 Clear transparent DACKQrOUNG ccceceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeeeeeeeeseeeeeeeseneaes 394 9 One click to Microsoft PowerPoint or WOIKd cccccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseaeeeeeesaneeeeseaneeeees 397 10 Embedding or linking Prism graphs in other programs ccccceeeeeeeeeeeeeeeeeeeeeeeeeeneeeeeees 399 AT LLINKBack MacCOnly ea a nezte nck feds cece a eae con ecgbenan yaddetcdsuddcwna weude ccu vedvencs vazeeecddutecnensexeer 404 12 Posting graphs to a Web Site cececeeeeeeeceeeeeeeeeeeeneeeeeeeeeneecenseneneeseeneeceeeeseneesanereneesoes 405 Part XXII Printing 406 1995 2014 GraphPad Software Inc e GraphPad Prism User Guide kh O N Part XXIII 1 2 Part XXIV a A OQ N Two toolbar buttons for printing ss ssssssssssnsssnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
2. 12 42 0 5679 7 42 3 471 17 96 0 8684 28 48 5 446 DO aT eae 23 Y 12 42 X 17 42 Y 17 96 X 28 48 Equation 2 5 What s new Time savers General time savers e Wand Wizard to analyze data After entering data onto an empty data table you often to analyze these new data exactly as you have analyzed another data table Prism has always provided a tool to do this but you probably never found it it used to be called Applying a Method Prism 6 introduces the Wand Wizard to ANalyze Data button Click it to analyze and graph a new data table just like you already analyzed and graphed an existing table Choose your own defaults Many dialogs now a have checkbox to make your choices on that dialog or tab become the defaults when you use the dialog in the future e Rename while duplicating a family A commonly used time saver is to duplicate a sheet with a family and then change the data in the new copy Prism 5 let you specify a prefix which then preceded all the newly created sheet names When the family only has one data table Prism 6 lets you entirely rename that data table e Faster saving Prism 6 Windows saves to a networked drive many times faster than did Prism 5 Prism 6 Mac saves over a SMB connection much more quickly e Faster closing Prism 6 Windows can close a large file much more quickly than did Prism 5 Make graphs faster e Easier to choose the rig
3. Nudge To prevent overlap move the selected data set Increment X by 0 00 data urits Incsement Y by 0 00 data ures hen axis is discontinuous also place gap n line Change Graph Type Hep Cancel App C ok 14 4 3 Nudging survival data sets Nudging data sets Nudging can be helpful to differentiate datasets that otherwise overlap a lot The Treatment B data set in the graph on the right has been nudged up a bit to separate it from the Treatment A data set 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 265 Appearance Data Sets on Graph Graph Settings The order of data sets in this list determines what happens when two date points overlap Data sets placed higher on this kst wil be graphed in front of data sets lower on the list Data sets plotted front to back tome of Three gioups Survival proportions A Coritrol Data on graph tee Tise groups Survival proportions C Treatment B Add Nudge To prevent overlap move the selected data set Increment X by 0 00 data urits 0 00 data units riirwous al pace gp n ine Hep Cancel Apo ox Treatment B Treatment B 120 Treatrent A 120 Treatment A 3 ei 3 S T E g 8 8 40 go 0 0 O 50 100 150 200 250 300 350400 0 50 100 150 200 250 300 350 400 Days after randomization Days after randomization 1995 2014
4. 1995 2014 GraphPad Software Inc sz GraphPad Prism User Guide Change ao GS e au X mif t EJ aH The excluded values appear in blue italics followed by an asterisk Group A Group B Data A Data B Excluding data sets If you want to only analyze selected data sets you can do so Don t exclude all the other points as explained above And don t expect your selection of data sets to matter when you click the Analyze dialog Instead you choose which data sets to analyze on the right side of the Analyze dialog You can change your mind later via Change Data analyzed Empty data sets How does Prism deal with empty data sets or data sets with all values excluded when analyzing data If you selected to analyze all the data sets the default then Prism leaves empty data sets in results if there are empty data sets in the data table That way the data set letter is always the same for data tables and results In other words the results for data set E are always in results data set E But if you selected to only analyze selected data sets Prism only analyzes selected data sets that are not empty If you choose to analyze data sets C D and E but data set D is empty then the results for data set C will appear in column A of the results table and the results for data set E will appear in column B in the results table 1995 2014 GraphPad Software Inc Analyzing data with Prism 325 16 7 Embedding results o
5. The figure below compares the appearance of decimal the default powers of ten and antilog formatting Decimal i gt H H H Antilog 10 100 1000 10000 100000 Powers of ten C rme e e eR 10 101 102 10 104 105 1995 2014 GraphPad Software Inc 314 GraphPad Prism User Guide In the graph below the X values represent the logarithm of concentration The logs were entered directly into the X column of the data table The graph of these data has a linear not log X axis The axis was formatted with a numbering format of powers of 10 and with nine minor tick intervals with log spacing see dialog settings below the graph 3 Percent Response 3 On ere or ee reer e rere or rr eran 170 107 105 10 10 10 Orug M In the graph below An alternative way to indicate that the data are logarithms is to choose the antilog numbering format this choice is only available when the interval is 1 the minimum is 9 or greater and the maximum is 9 or less E S 7 1000 3 S a v 5 e 3 g 2 Pomet Ankg 04 eee 0 001 0 01 0 1 1 10 100 1000 Concentration nM 15 3 8 A review of logarithms Common base ten logarithms The best way to understand logarithms is through an example If you take 10 to the third power 10 x 10 x 10 the result is 1000 The logarithm is the inverse of that power function The logarithm base 10 of 1000 is the power of 10 that gives the
6. Gaps andDiectore Standeed X Scale Linear Automatically determine the range and interwal Range Minimum 20 Maxinurne All ticks Ticks Grectiors Lett X Location of numberng labelng Lett horizontal X Ticks length Shot gt Regulatly spaced ticks Mar ticks ntervak 100 0 Format Decimal X Auto decimal places Starting at Y DO Thousands 100000 Minor licks 0 mn v log Prefec Suthe Additign Show additonal ticks With regula bcks ps6518 Instead of regular ticks Only regular ticks 1995 2014 GraphPad Software Inc Graphs Frame and axes 293 Effect of GP 41152 on ap Receptor Number Specific Binding tmol mg Kd 5 10 15 20 Hy Yohimbine nM To format an additional tick Details Ami Click on the Details button of the Additional Ticks and Grid Lines section of the Format Axes dialog This appears as a gear on Prism Window and as on Prism Windows This lets you format how the tick or grid line will look and add text to the label Format Additional Ticks and Grids Select one or more ticks y SelectAll ALY 257e0005 F Show Text Tewtline 1 Kd 4 Text line 2 d i Location Auto X x E Show Tick i Manr Auto i Aut i i F Show Grid Line Thickness lpt Style i i Color Ato Under data points f Fill shade between this tick and Y y New Tick Delete Tick n a Under data poi
7. SetAxisLimits Y top 200 SetAxisLimits Y bottom 100 SetAxisLimits Y interval 10 If the Y axis was split into two segments you need to specify which segment to change The first left or bottom segment is 0 and the second segment is 1 If you wanted to change the bottom segment use these commands Note that it is not enough to specify the segment number you also need to include the word segment SetAxisLimits Y segment 0 top 200 SetAxisLimits Y segment 0 bottom 100 SetAxisLimits Y segment 0 interval 10 23 2 8 Setting the default drive and folder Commands SetPath drive and folder path Explanation All the commands that read and write files use the path set in the SetPath command unless you specify a different drive or folder in the other commands For Windows use these examples SetPath My Documents 007 goldfinger oddjob SetPath C DataFiles August2005 SetPath LabServer DDrive PrismFiles The last example opens a file on another computer named LabServer In this case you don t use the C notation for hard drives but rather refer to the name of the drive DDrive in this example 1995 2014 GraphPad Software Inc 426 GraphPad Prism User Guide On the Mac use a format like this SetPath Hard Drive Prism 4 Data June21 If you prefer to specify the path within each individual command you can still use the same formats as shown above 23 2 9 Opening
8. 1000 100 Control Treated Control Treated The relative height of the bars appears to be almost the same in the graph on the right and very different on the graph on the left The relative heights or areas of the bars on a log scale is not informative If the goal is to create propaganda a bar graph using a logarithmic axis is a great tool as it lets you either exaggerate differences between groups or 1995 2014 GraphPad Software Inc 312 GraphPad Prism User Guide minimize them All you have to do is carefully choose the range of your axis to give the impression you want to project If your goal is to honestly show the data don t create bar graphs using a logarithmic axis The only case that I know of where it makes sense to plot bars ona logarithmic axis is when the Y axis is plotting the fold change in something Then the baseline of 1 0 is logical no change as is a logarithmic scale 15 3 7 Graphing logarithms different than using a log axis Transforming data to logs If you need log data for your analysis you can either enter logs directly or transform your data For example you should fit a sigmoidal dose response equation to data expressed with X as logarithm of dose If you enter concentrations you ll need to convert them to logarithms before using nonlinear regression To transform your data to logs Click the Analyze button choose built in analyses and then select Transforms from the list of d
9. Prism files 107 You can send a Prism file even to someone who doesn t own Prism The recipient can view the file using either the free Prism demo or the Prism Viewer both available from www graphpad com The Viewer doesn t expire It lets anyone view and print all contents of a Prism file including analysis choices but does not allow any editing or exporting 8 6 LabArchives A labarchives Chance Favors the Organized Lab Far more than an ELN Electronic Laboratory Notebook LabArchives stores and catalogs all of your research for easy retrieval and publication Registered users of Prism can obtain a free account on LabArchives To set up this account go to a graph in Prism click the LabArchives button to drop a menu and choose to LabArchives it You will be prompted for your email address which is all you need to start an account You do not need to enter a credit card number m LabArchive it Ctri Alt A Browse My LabArchives Learn about LabArchives T Prism 6 integrates well with LabArchives e Click LabArchive it to upload files directly to LabArchives e When it uploads a file to LabArchives Prism also sends LabArchives a list of all words used in notes titles text boxes etc That mean you can search within LabArchives to find the file you need e From the Welcome dialog of Prism 6 you can open a file directly from LabArchives There is no need to first go to labarchives com to download the
10. 1995 2014 GraphPad Software Inc za GraphPad Prism User Guide Plotting order of Grouped graphs Additional Grouped graph settings Replicates and error bars on Grouped graphs 14 3 1 Appearance of Grouped and Contingency graphs Format Graph dialog Grouped graphs Use this dialog to change the look of all the columns in a data set If you want to change the look of a single column use the right click menu You can also change all the symbols in selected data sets Double click on any graph symbol or bar to open the Format Graph dialog 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 245 f Format Graph Appearance Data Sets on Graph Graph Settings Data set First look grouped data Treatment x H lt gt Global Style Appearance Bat Pict Mean with SEM X Bars and boxes Fi a Palem ERR v Pattem color Border 2 pt Border color ME Symbols Color M shape O es Size 4 E X Eror bars Cole ME Stile TO o Dit Both Thickness 2ppt X Lines es E pt n top Additional options Plot on Left Y axis Show legend Revert legend to column title Right Y axis abel each point with its row title Change Graph Type Help Cancel Apply To change the settings for one data set Select a data set from the list and choose the symbols lines and error bars for that data set Then select another data set and choose settin
11. Linear F Automatically determine the range and interval Range row numbers tis not possible to change the range of this ads All ticks Ticks drectior Dom Location of numbering labeling Below ended Ticks length Shot Numbetingabeling angle 452 Regularly spaced ticks Major ticks irtervat 1 Prefic i Stating at X 1 Decimalz Auto i Sutic Miner ticks bg Thousands 10000 Additional ticks and grid lines it is not possible to creste additional ticks or gndines on this aas 1995 2014 GraphPad Software Inc 25 GraphPad Prism User Guide Row Titles Column Titles 450 MM Wilctype cells 150 EE ilti pe cells GPP5 cell line GPP5 cell line Signal Signal E s Fa O lt gt f amp 14 4 Survival graphs Formatting options Format graph Survival Prism lets you change every feature of a graph Change the shape color and size of graph symbols change the fill pattern and color of graph columns change the order that data sets are plotted Double click on any symbol or bar or the background of the graph to bring up the Format Graph dialog See also Survival graphs formatting options Appearance of Survival graphs Changing the plotting order of data sets Nudging survival data sets Error bars and confidence bands on Survival graphs 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 259 14 4 1 Appearance of Survival gra
12. Origin Set ign Automaticaly zj Y intersects the X ads at X X ntersects the Y ads at Y 0 Shape Size and Position Height Length of Y as Axes and Colors Thickness of axes lpt Color of axes i Frame and Grid Line Graphs Frame and axes Size Wide Distance of Y axis from left edge Width Length of X axis Distance of X axis from bottom edge Color of plotting area Page background Frame style No frame a Hide axes Show both X and Major git None Color eee Thickness 1 pl Style Minor grid Color Thickness Style 15 1 2 Customizing a graph s frame and axes appearance Double click on the graph origin to open the Frame and Origin tab of the Format Axes dialog 1995 2014 GraphPad Software Inc GraphPad Prism User Guide la Format Axes Frame and Origin x anis Left Y axis Right Y axis Tiles amp Fonts Origin Setongn Automatically z Y ntersects the X ads at X X ntersects the Y aasatYe 0 0 Shape Size and Position Size Wide X Distance of Y axis from lelt edge 275 in Width Length of X axis 3 00 in Distance of X axis from bottom edge 4 49 in Height Length of Y aas 200 in Axes and Colors Thickness of axes ip Color of plotting area Clear Color of anes ia Page background Clear Frame and Grid Line Frame style No frame z Hide axes Show both X and Y gt Show Scale Ba Major gi None
13. Range Mnimum 40 0 All ticks Ticks Grector Lett Ticks length Sheet Regularly spaced ticks Mar ticks nterval 10 0 Starting a Y Minor ticks A Additional ticks and grid lines ALY Tick z zj Une Frame and Origin x axis Left Y axis Right Y avis Tiles amp Fonts Scale Linear X V Automatically determine the range and interwal Marinum Location of numberng labelng Lett horizontal X Format Decimal Auto w decimal places Thousands 100000 log Pref Suth Text Forts Greek aia a Show additonal ticks With regular bcks z Instead of regular ticks Only regular ticks You don t want to enter a Y coordinate on the Format Additional Ticks and Grids dialog Instead you want to hook an analysis constant Click on the hook button and then choose the value you want to hook first the mean later the two QC control lines Back on the Format Additional Ticks and Grids dialog choose the kind of line solid or dotted and its color You can also choose to fill between the two QC lines 1995 2014 GraphPad Software Inc Analyzing data with Prism 331 Text line 2 Location Z Show Tick Size Maor Drechon Auto C Show Grid Line Thickness 1 2 pt Color Fedo Under data points T Fill shade between this tick and Y ss Fil color v Paten New Tick Delete Tick Pattern color BE Under data points 1995 2014 GraphPad Software Inc 332 G
14. You use nonlinear regression to fit a dose response curve to six data sets The first three A C are for one drug the other three are for another D F The logIC50 values are all on one row You know tha the first three are for one drug and the next three for another But Prism doesn t know this The results look like this 1995 2014 GraphPad Software Inc Importing and exporting data 161 Best fit values Bottom froas Top iC long Top __ 097 6225 6035 5943 5812 5849 LoglC50 5 979 6 542 6 322 6 404 You want to put the logIC50 values into a new data table The first three should go into column A and the next three into column B Follow these steps 1 Select the six values 2 Copy them to the clipboard 3 Use New Data table and graph to make a new Column table 4 Put the insertion point into Column A and Row 1 of that new table 5 Choose Paste Special from the Edit or right click shortcut menu 6 On the first Source tab of the Import and Paste Special dialog choose to insert and maintain link 7 On the fourth Placement tab of that dialog choose to paste by columns stacking 3 values in each column That way the six values that you copied as one row will paste into two columns 8 Click OK 9 Note that the values pasted into the data table are surrounded by a red box You cannot edit these values on the data table If you double click within that box you ll return to
15. lt delimiter gt Explanation These commands make it easy to export Prism results into structured tables The first step is to define your table Choose to place the results into a data table within Prism to a text file delimited with tabs to a CSV text file delimited with commas to a HTML web table to an XML table or directly to a ODBC connected database If you choose to write to a text CSV or HTML file create the file using the OpenOutput command before creating the table This lets you combine other information as explained in the next section as well as the table XML output must be in its own table so enter its file name as part of the Table XML command Use the WTable command to write a value into the table The first argument will become the column title in the new table or the variable name when exporting to a database The next three arguments define the cell on the current results or data table that will be written to the new table Or enter text to just space columns apart or N to put in the loop number or F to put in the current file name 1995 2014 GraphPad Software Inc Note that the Wtable command has a name that can be misleading It writes a single value or text string to a table The command does not write an entire table If you want to write an entire results or data table use the WSheet command In almost all cases you ll create a table as part of a loop The Next statement that ends t
16. Appearance Data Sets on Graph Graph Settings Direction Vertical Horizortal Baseline tomatic Bars begin at Y lide baseline Dimensions Space between columns 50 of column width Discontinuous axis Format of individual points To format a data point differently than the rest ext thes dialog night click on the data point and choose Foemnat This Point Remove all the individual formatting Revert all data points to the format of thei data sa L One point has individual foematting 13 12 Changing a graph s shape and size Stretch an axis Click on the axis to select it Knobs appear on both ends Move the mouse over the right knob of the X axis or the top knob of the Y axis Drag the axis to make it longer or shorter Specific Binding tm omg lt gt 0 0 s 100 150 Concentra ton KvP pM 1995 2014 GraphPad Software Inc 208 GraphPad Prism User Guide Enter the exact length of the axes Double click on the origin to bring up the Frame and Origin tab of the Format Axes dialog Select a custom shape and enter both width and height Or select a standard tall square or wide shape enter either height or width and Prism will automatically change the other value On a wide or tall graph the long axis is 1 5 times the length of the short axis Format Axes Fiame and Origin X amis Lett Y axis Right Y axis Titles amp Fonts Ongin Set ongin Autom
17. The scaling factor is defined as the ratio of the size of the graph on the layout compared to its size on the graph If the graph and layout are zoomed differently it will be hard to understand the scaling factor Set the zoom to be the same for the graph and layout using controls in the lower right of the Prism Window Changing the scaling factor of one graph The easiest way to change the scaling factor is to select a graph on a layout page grab a corner and drag If you want to set the scaling factor to a particular value double click on the graph on the layout to bring up the Place Graph on Layout dialog Go to the second Size and Location tab and set the Scaling Factor 1995 2014 GraphPad Software Inc Page layouts 365 Place Graph on Layout Assign Graph Sge and Location Hint You can diag and stretch graphs and placeholders on the layout tsef so the choices below are only needed in special situations Scaling Factor Size on Layout ScalngFactor 80 Se in Graphs section Location on page Distance from beitedge 056 in Distance from topedge 056 in Rotation Noemeal 90 degrees clockwise depth chait 90 degrees counter clockwse Border Thickness None z Coor RR Siye Hep Cancel oK Note that this tab also lets you specify a border to go around the graph Equalize the scaling factor of several graphs 1 Select the graphs to equalize not necessary if you want
18. toolbar Text 14 Arial v A a B U x ji oS To move a title 1995 2014 GraphPad Software Inc Graphs Frame and axes 299 Move the mouse near the title until the cursor turns into a two headed arrow Then hold down the primary mouse button and drag the title into position Alternatively go to the Titles and Fonts tab of the the Format Axes dialog where you can position the title by entering the desired distance between the axis and the title A graph title is always centered over the graph and an axis title is always centered on the axis If you want noncentered titles delete the title and then create a separate text object which can be positioned anywhere To hide a title or rotate a title Double click an axis to open the Format Axes dialog Uncheck options to hide any of the titles For both Y axes you have the choice to make the title vertical or horizontal m Format Axes Frame and Origin x axis Left Y axis Right Y wis Titles amp Fonts Graph title Show Graph Title Font Distance from top of graph 00 n Axes titles Font Distance from axis 028 in J Show Left Y axis Title Font Distance from axis 037 in Direction Vertical Up Distance from axis lin Direction Vertical C Numbering and labeling X axis Font Distance from axis 0 00 in Left Y axis Font Distance from axis 00 n Right Y axis l Distance from axis n To change the default font and siz
19. Double click on the X axis to bring up Format Axis Choose to make the axis scale logarithmic with log spaced minor ticks and to create a grid line at X 1 0 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 243 f Format Axes jei Frame and Ongin X axis Left Y axis Right Y axis Titles amp Fonts Gaps and Direction Standard gt Scale Log 10 z J Automatically determine the range and interval Range Minimume 01 s Maxim 0 0 A All ticks Ticks drection Dom v Location of numbeting abeling Below horizontal Ticks length Shot Numbeting labeling angle Regularly spaced ticks Manor ticks intervat 11 0 powers af 10 Number format Antlog Starting at X 7 Decimats 0 01 0 1 1 10 Minor ticks 7 bog AUX Tick Line Text Forts Greek Details Show additional ticks 1 J Wh regular ticks Instead of regular ticks Z Only regular bcks 14 3 Grouped amp contingency graphs Symbols and line formatting Format graph Grouped and contingency Prism lets you change every feature of a graph Change the shape color and size of graph symbols change the fill pattern and color of graph columns change the order that data sets are plotted Double click on any symbol or bar or the background of the graph to bring up the Format Graph dialog See also Appearance of Grouped and Contingency graphs Data set grouping and spacing on Grouped graphs
20. Exit loop if no more files Beep Signal completion 23 1 3 Script example 2 Monte Carlo analysis This is an example of Monte Carlo analysis We ll simulate 500 data sets with random variation and fit a dose response curve to each This script creates a table containing the logEC50 and HillSlope from all 500 fits Before running this script you must create a file that has the first data table formatted for a one grouping variable data set no X No Y subcolumns The first results sheet must be one that simulates data with error The second results sheet must be a nonlinear regression that fits a dose response curve to the data Script command Comments Table Prism 1 Clear Designate the first data table in your file to contain the results of this script Delete all the contents of that table now clear Note this script requires that the first data table be formatted for one grouping variable data with no X column ForEach 500 Loop 500 times GoTo R1 Go to the first results sheet which is a simulation Regenerate Regenerate the simulation with new random numbers GoTo R2 Go to the second results sheet Since this sheet contains nonlinear regression results Prism will automatically refit the data for each loop 1995 2014 GraphPad Software Inc se GraphPad Prism User Guide Wtable logEC50 5 1 Write the value from the first Y column in row 5 to the first column of the output table and label that column log
21. GraphPad s entire liability and your exclusive remedy will be at GraphPad s option to attempt to correct or work around errors to replace the defective media on which the Software is furnished if any or to refund the license fees if any paid by you and terminate this Agreement DISCLAIMER OF WARRANTY EXCEPT AS SPECIFIED IN THIS AGREEMENT GRAPHPAD 1995 2014 GraphPad Software Inc 466 GraphPad Prism User Guide MAKES AND YOU RECEIVE NO WARRANTIES EXPRESS OR IMPLIED WITH RESPECT TO THE SOFTWARE AND THE USER DOCUMENTATION ANY STATEMENTS OR REPRESENTATIONS ABOUT THE SOFTWARE AND ITS FUNCTIONALITY IN THE USER DOCUMENTATION OR ANY COMMUNICATION WITH YOU CONSTITUTE TECHNICAL INFORMATION AND NOT AN EXPRESS WARRANTY OR GUARANTEE IN ADDITION GRAPHPAD SPECIFICALLY DISCLAIMS ANY OTHER WARRANTY INCLUDING WITHOUT LIMITATION THE IMPLIED WARRANTIES OF MERCHANTABILITY FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT WITHOUT LIMITING THE FOREGOING GRAPHPAD DOES NOT WARRANT THAT THE OPERATION OF THE SOFTWARE WILL BE UNINTERRUPTED OR ERROR FREE SOME JURISDICTIONS DO NOT ALLOW LIMITATIONS ON IMPLIED WARRANTIES SO THE FOREGOING MAY NOT APPLY TOYOU THIS LIMITED WARRANTY GIVES YOU SPECIFIC RIGHTS OTHER RIGHTS WHICH VARY FROM JURISDICTION TO JURISDICTION MAY APPLY TO YOU LIMITATION OF LIABILITY INNO EVENT SHALL GRAPHPAD HAVE ANY LIABILITY FOR ANY INCIDENTAL SPECIAL INDIRECT OR CONSEQUENTIAL DAMAGES LOSS OF PROFITS REVEN
22. Inc Exporting images from Prism 383 There are several ways to get your graphs and layouts into other applications You can export them to PowerPoint or Word using one click export You can export them in a variety of image formats or you can copy and paste your graphs and layouts as bitmaps 1995 2014 GraphPad Software Inc 384 GraphPad Prism User Guide 21 1 How to export one or more graphs or layouts Are you sure you want to export If your goal is to send graphs to a colleague who doesn t own Prism consider sending a Prism file He or she can then open the file using Prism itself the free Prism demo expires in 30 days or the free Prism viewer never expires If your goal is to place graphs into a Word document or PowerPoint presentation you can copy and paste or use the one click send buttons rather than exporting There are some settings in the Prism Edit Preferences menu that will affect the result and whether or not you will paste your graph as a Prism object or a picture Read more about copy and paste settings Also note this easy to bypass bug in PowerPoint 2007 How to export 1 Start from one graph or a layout or from several graphs or layouts selected on the Gallery 2 Click the Export button on the Prism toolbar to bring up the Export Graph dialog Alternatively drop the File menu and choose Export Export TIFF EMP 3 Choose the export format and also choose the location and name of
23. Prism projects can have many data tables You are not limited to one data table per file Store an entire project in one file creating as many data tables as you need Prism can compute error bars Prism can plot error bars from raw data You don t have to enter SD or SEM values although you can 9 2 Prism s six data table formats The format of a Prism data table determines what kinds of graphs you can make and what kind of analyses you can perform Choosing a data table format lets Prism create a data table that fits your data and makes it easy to create the kind of graph you want and perform the appropriate analyses You can always change the format of a data table The six kinds of data tables XY tables An XY table is a graph where every point is defined by both an X and a Y value This kind of data are often fit with linear or nonlinear regression 1995 2014 GraphPad Software Inc Distinguishing the six kinds of data tables 111 x A j mirates Test group A C p e 0 00 00 00 2 391 0 384 0 5430 4 5620 478 0 5840 6 748 0 798 0 7150 8 8230 754 0 689 0 10 736 0 846 0 7420 12 320 855 0 793 0 14 9230 750 0 8160 16 8010 854 0 826 0 18 8110 795 0 864 0 20 9420 831 0 938 0 ee i ele ee eee ee ee ees Column tables Use column tables if your groups are defined by one scheme perhaps control vs treated or placebo vs low dose vs high dose Each column defines one group 45 67 23 46 56 113
24. Size on Layout Scaling Factor 80 cert ak teeta Size in Graphs section Location on page Distance from leftedge 057 in Distance from topedge 057 in Rotation Neemal 90 degiees clockwise depth chart 90 degrees counter clockwae Thickness None Color ME Style The result on the layout is a depth chart with the X variable on the vertical axis and the Y variable and its error bars plotted on the horizontal axis 1995 2014 GraphPad Software Inc Page layouts 369 pO 0 50 100 150 0 eH N E 2 Ke rT HH S 4 4 7 A m 6 re 19 7 Master legends one legend for several graphs If you place several graphs on a layout you can create a master legend that applies to all the graphs as shown below ren ome It took four graphs to make this figure The first three graphs show data and the fourth not shown was used only to create the master legend Follow these steps 1 Duplicate one of the graphs to create another graph that won t be shown in the layout but will be used to create a legend To create a legend on this graph double click on a symbol to bring up the Format Graph dialog Click the Global button to change all data sets Then check Show Legend 1995 2014 GraphPad Software Inc GraphPad Prism User Guide 2 Create a layout and assign the graphs three in this example 3 Select and copy the legends from the extra graph and paste onto the layout Paste Drawing That is
25. So when you want to make a second graph of that same data people commonly copy the data and paste onto a new table which is automatically graphed No need for that You can make any number of graphs from the same table Just click the New button and then choose Graph of Existing Data Mistake Repeatedly formatting a series of related graphs No need to change the fonts colors line thickness etc etc for each graph in a series Instead format one graph and use Magic Make Graphs Consistent to instantly fix the others Mistake Making a project too large We call a Prism file a project but you can decide how large to make it Huge files can be hard to navigate So it often makes sense to keep files of reasonable size You can always merge projects later or include a graph from one project in a layout of another Mistake Going through many steps to make the same graph from a new data set There is no need to repeat yourself Once you have a graph you like Prism offers several ways to make that graph again with different data Start by learning to clone a graph 1995 2014 GraphPad Software Inc Getting started with GraphPad Prism e a Mistake Not saving milestone backups while working on a large project When working on a large project do more than backup the current version What happens if you mistakenly delete key data What happens if the file someone gets corrupted Use Prism s Backup command to save inter
26. There is no way to empty the search results folder Just use the Search command or button again to search for something else 1995 2014 GraphPad Software Inc GraphPad Prism User Guide Navigator tool tips If you ve got lots of sheets in a project and you re not sure which one you are looking for hover your mouse over any sheet name in the Prism Navigator to display a thumbnail of the sheet LE tapie OF resums lA Curve ii Graphs k Data 1 graph k Transform of Data 1 graph fle Normalize ii Layouts je Layout 1 Wh Floating Not 5 5 Changing the zoom Zoom buttons Use the Zoom buttons located on the lower right side of the Prism screen to enlarge or shrink the view of the current sheet You can also use the Zoom tools to make thumbnails in the Gallery larger or smaller QQ On graph and layout sheets Zooming lets you see more or less of the sheet but doesn t change the size of the graph or layout when printed Click here to find out how to actually resize graphs and layouts On data tables and analysis results sheets the Zoom buttons not only change what you see but they also actually change the size of the font Prism uses when you print If you want to get more of your data table on a printed page Zoom Out to make the font smaller Keyboard shortcuts 1995 2014 GraphPad Software Inc Getting around in Prism 7z Shortcut Hold the Ctrl key and press M to zoom larger or J to zoom smaller M
27. They also provide links to take you to other parts of the project Hover your mouse over a symbol on a graph to see the value and location of the data point Click on the name of the data or results table to go right to the correct spot on the data table Enzyme kinetics Right click to reformat this point 0 0 20 40 60 80 100 120 140 Substrate mM Hover your mouse over any graph on a Layout A tool tip will appear with a link to the graph Click on the link to go to the graph 1995 2014 GraphPad Software Inc Getting around in Prism Date 1 1 07 Prospective espriin end M MME Trested 12000 GE Myocardial Infarction C AAA Placebo Aspirin Survival of Two groups Survival proportions Control sen Tesed 186 Tested 0 0o 10 2 3 4 50 60 0 0 400 150 200 250 Mrates Days ste reccomizaion 5 4 Tools for navigating large projects A Prism project file can have up to 500 data tables info tables analyses graphs and layouts Lump lots of data into one file Or split into many files The choice is yours If you prefer to create large projects use these tools to navigate Use the bottom toolbar Browse the sheets sequentially He a lwo Ping pong between any two sheets Click once to go back to the previous sheet Click again to return lt gt n ee a 8 Pick from a menu of sheets linked to the current sheet or use the five tabs to jump between sec
28. To change all or some data sets on the graph for example to make all symbols larger Drop the list of data set names and choose Change ALL data sets Or click the Global button just to the right Changes you make after that will then apply to all data sets or to data sets you select from the Global button Style 1995 2014 GraphPad Software Inc 226 GraphPad Prism User Guide Choose how you want to display your data for each data set Choose from a simple bar with or without error bars a scatter plot an aligned dot plot box and whiskers before and after plot or floating bars Also choose how to plot error bars Select SD SEM 95 CI or range Note that your choice applies to only one data set column unless you used the global button to choose all or a subset of columns 3883338388 os88sS8a88s eSB 858838 es88sssssss It can Cats Dogs Hamsters Or connect data sets A and B as before and after and data sets C and D but not B and C 16 14 12 on 22 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 227 To do this choose Before and after as the style for data sets A and C and Scatter dot plot as the style for data sets B and D Box and whiskers plots Style Appearance Box and whiskers wihiekews dilins MMe nnn Bars and boxes Yaer Max ra Pater ME Segre 2597 5 percentile 1 99 percentile Min to Max Show all po
29. To plot data using the right Y axis Double click on a data point or click on the Format Graph button on the Prism toolbar At the bottom of the Appearance tab select Right Y axis Repeat for each data set to be plotted on the right Y axis If you assign a data set to the right Y axis and there is no Y axis Prism will auto matically create the axis Ferrat Crap Appearance Data Sets on Graph Graph Settings Data set Data 1 Tieate Ha Global Style Appearance Mean onhy Plot Show symbols Coor E Shape E gt BRRR a See 4 E 2 pt Show bars spikes droplines SE CU Show error bars aes Show connecting line curve When ax ccontnuous also place gap n ine Leave gap at symbo Show area fill Plot or Lett Y ans Show legend Right Y axis Revest legend to column title Label each point with ts row title Help Cancel Appy OK To create a graph with ONLY a right Y axis Turn off the left Y axis and create a right Y axis to which you assign data set 1995 2014 GraphPad Software Inc 286 GraphPad Prism User Guide Format Axes Frame and Ongin X anis Left Y axis Right Y ans Titles amp Fonts Gaps and Director Scale Linear X a Automatically det 4 Range Two segments Minimum Three segments 7 Maximum All ticks To use different colors for the two Y axes It is possible to give the two Y axes differ
30. When you paste an object created by a program that is an OLE server Prism will embed the object This means that Prism contains a separate copy of the object In some cases you may prefer to paste link to the original file To do that copy the object and then choose Paste Special from the Edit menu Then choose Paste Link To learn more about the pros and cons of linking and embedding see Object linking and embedding To create an equation using Microsoft Equation Editor Write a T amp To insert a new object created by a program that is not on Prism s toolbar Windows only Drop the Insert menu and choose Insert Object Choose Create New and select the 1995 2014 GraphPad Software Inc Adding text drawings and pictures to graphs or layouts 377 program you wish to use The list shows all programs on your computer that can create objects Create the object in the selected program which will run in a small window on top of Prism After creating the object close that application to return to Prism In some cases the application appears as a dialog which you close by clicking OK In other cases it appears as an application that you quit by dropping the File menu and choosing Exit and Return To import a graphics file Use the File Import command to import a picture Prism Windows can import Windows Enhanced Metafile emf Windows Metafile wmf TIFF tif tiff JPEG jpg jp2 j2k jpx Po
31. a period point is used as the decimal separator In other parts of the world a comma is used When entering data into Prism you can use either a period or a comma to mark the decimal point When exporting data Prism uses the separator you choose in the Export dialog When pasting data Prism uses the separator set in Preferences When importing data you can specify how a comma is interpreted as a decimal separator as a thousands separator or to separate columns of data 1995 2014 GraphPad Software Inc Data tables 139 10 11 Excluding data table values from graphs and analyses Excluding values from data tables If a value is too high or too low to be believable you can exclude it Excluded values are shown in blue italics on the data table but are not included in analyses and are not shown on graphs From the point of view of analyses and graphs it is the same as if you had deleted the value but the number remains on the data table to document its value To exclude selected values Click the Exclude button from the Change toolbar Change a E X mf t EJ at The excluded values appear in blue italics followed by an asterisk Group A Group B Data A Data B Choose on the File amp Printer tab of the Preferences dialog how excluded values should appear when copied to the clipboard Your choices are to copy a blank value as if missing a regular number ignoring the fact that the value is excluded
32. about error bars on XY graphs 1995 2014 GraphPad Software Inc GraphPad Prism User Guide 7 Show error bars ni A Mom T Tl thicker Show connecting line curv T fatineatoig a efor ea bcol Show area fill 20 25 2 15 10 5 0 0 5 10 15 2 25 Connecting line curve Choose the line s color style straight vs staircase thickness and pattern solid dotted dashed etc This section includes choices to have your connecting start either at the first data point or the graph origin whether to leave gaps in the connecting line next to the symbols and whether to plot lines connecting each replicate for repeated measures in corresponding data sets as in the graph on the bottom row below 30 25 25 25 20 20 20 15 i 15 15 10 z i 4 pd 10 5 5 5 0 a 2 3 4686 e 23 4 6 6 e 23 4 8 amp 35 30 25 20 15 10 If you choose arrows as connecting lines it looks best to not also show symbols 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 217 Don t confuse the connecting line which always goes from point to point with a best fit curve or line created by regression If you have fit a curve through the data Prism sees the curve as a Separate data set Select the data set for the values and choose symbols but no connecting line Then choose the data set for the curve and choose a connecting line curve with no symbols Area fill
33. an object or a linked picture Microsoft Word and Excel and older versions of PowerPoint paste an embedded object PowerPoint 2007 and 2010 are different By default they paste a picture To override this drop the clipboard menu choose Paste Special and then choose to paste a Prism object Copy and Paste Special Instead of pasting and letting the program choose use the Paste Special command so you can choose which format is pasted With most programs Paste Special is a choice on the Edit menu With Office 2007 and 2010 itis a choice on the Paste menu which is on the left side of the Home tab of the ribbon Paste Special Source GraphPad Prism 5 Project As GraphPad Prism 5 Project Obiect C Display as icon Bitmap cture Enhanced Metafie Inserts the contents of the Clipboard into your document so that you can edit it using GraphPad Prism 5 Project n The scrolling list lets you choose to paste an object GraphPad Prism 6 Project Object or a Picture Enhanced metafile You can also paste a bitmap which might be useful if you want this Word or PowerPoint document to look nice on a Mac The left side of the dialog offers the option of pasting a link If you check this option the scrolling list gives you no choices This option will not be available if you copy a graph from an unnamed Prism project because linking requires that the Prism file has a name The right side of the dialog offers the option of
34. and legends 241 Snow 1999 Raine 2003 Shon 2002 Odds ratio There are a few tricks to making this graph 1 Enter the data into a Column table The results for each study are entered into a separate data set column Enter in each column the Odds ratio itself as well as the high and low confidence limits computed elsewhere The order of those three values doesn t matter Label the studies by entering column titles You may use Greek symbols super and subscript etc A B C 1 0 7 1 2 2 1 a cmt ORE 2 When you first go to look at the graph Prism will prompt for the kind of graph you want Choose Column Mean with error bars To make the graph above be sure to choose the option where the error bars go horizontally 1995 2014 GraphPad Software Inc 242 GraphPad Prism User Guide Change Graph Type Graph family Column ie a i HH Column mean error bars Plot Median withianse v 3 Note that Prism s doesn t can t know that each column contains a computed odds ratio along with the low and high confidence limits It just sees three values So choose to plot the median and range The median and range of the three values you entered are the odds ratio and its confidence limits computed elsewhere If you choose to plot a confidence interval instead Prism will compute a confidence interval from the three values you enter and the results will be nonsense 4 View the graph
35. file you want LabArchives usually uses a server maintained by LabArchives 1995 2014 GraphPad Software Inc 108 GraphPad Prism User Guide If you want to use a local server to host LabArchives files you can do so Details here 9 Distinguishing the six kinds of data tables Unlike the data tables of most programs the data tables in Prism have a format or structure There are six different kinds of tables and it is 1995 2014 GraphPad Software Inc Distinguishing the six kinds of data tables essential that you pick the right one for your data and experimental design 9 1 Key concept data tables Choosing among the six kinds of data tables is important The format of a Prism data table determines what kinds of graphs you can make and what kind of analyses you can perform Choosing the right kind of 1995 2014 GraphPad Software Inc no GraphPad Prism User Guide table for your data is really important Take the time to get this right Don t try to choose the right kind of table for your data by thinking about the kind of graph you want to make That approach will end up confusing you because there isn t a one to one match between table and graph types For example you can make a bar graph from four kinds of tables and a a graph showing points a scatter graph from three kinds of tables You need to choose a table based on the organization of the data and the analyses you wish to perform
36. file_path You can create an icon that will open a Prism file and print all pages Edit the Prism start icon to add the P switch so the target looks like this Please note space between P and file_path Prism prints silently without Prism appearing in the taskbar C Program Files GraphPad Prism 6 prism exe P c test pzf Use custom option file O prism_cfg_file_path 1995 2014 GraphPad Software Inc Support and license as Prism stores many settings in a preference file also called an options file This file contains all the settings in the Preferences dialog a list of recently used files user defined equations color schemes and more You can use a startup option to force Prism to access the preferences file from a different location This might be useful if you use Prism for several very distinct uses and want a separate set of preferences for each It would also be useful if different people use Prism and each wants unique preferences but they all want to log in to Windows as the same User To tell Prism to use a unique preference file edit the Prism start icon to add the O switch so the target looks like this Please note the space between O and file_path C Program Files GraphPad Prism 6 prism exe O c gsconfig cfg Don t save preferences C Prism stores many settings in a preference file also called an options file This file contains all the settings in the Preferences dialog a list of rec
37. number of characters The limit is 64 000 characters If you hit this limit consider removing comments and blank lines Also consider removing any parts of the script that are not needed For example most script commands have default parameters and if these are correct you don t need to hard code parameters 1995 2014 GraphPad Software Inc GraphPad Prism User Guide 24 Standardizing Prism use in a lab If many people in your lab use GraphPad Prism you may want to standardize some preferences or provide all with a set of templates or equations or color schemes This section explains how to do SO 1995 2014 GraphPad Software Inc Standardizing Prism use in a lab 449 24 1 Locking the preference file What is included within the preferences file Prism offers many choices on its Preference dialog It allows you to set defaults for color schemes fonts symbols sizes graph units and more Beyond that the Prism Preferences file remembers which files you have recently opened or closed user defined equations you have created color schemes you have created autocomplete text and more All that is saved in a preference file that customizes Prism for you Where is the preference file located Windows XP system disk Documents and Settings user Application data GraphPad Software Pri Vista and Windows 7 system disk Users user AppData Roaming GraphPad Software Prism 6 0 Prism6 cfg Mac local
38. or a value followed by an asterisk to match what you see Prism offers the same choices on the Export dialog to control how excluded values are exported to TXT or CSV files Outlier elimination Instead of manually choosing points to exclude you can ask Prism to perform outlier elimination Removing entire data sets To remove a data set from a Graph click on the Add Remove data sets button from the Change toolbar Select the data set to remove This dialog will also let you add data sets to a graph 1995 2014 GraphPad Software Inc 140 GraphPad Prism User Guide Change P tt jit aaa Ls Ti MAN KOS amp To remove a data set from a Results sheet click on the Analyze different data sets button from the Change toolbar and choose the data sets to include in the analysis Change Analyze Data Data to analyze Tabie Data 1 Type of analysis Which analysis Transform Normalize 10 12 Missing values Analyze which da sets J Activin J 8 Activn When entering data simply leave a blank spot for any value that is missing Excluded values are treated exactly the same as missing values Prism never ever treats an empty cell as if you had entered zero it always knows that is a missing value It will analyze the data if it can and leave analysis results blank when it cannot The details of how Prism handles missing values differs for various statistical tests Unpaired t test
39. pastes in a form that is mac only If you open the project in Windows that graph will be missing from the layout Use an option in the Files tab of Prism Preferences to save in a compatible format On the Mac you will notice that the files will be larger and pasting graphs from other projects will take longer but still only a few seconds Now the file will open fine in Windows e If you dictate audio notes to embed onto a graph or layout of Prism Windows those audio notes will not be present when you open the file on the Mac e Tabs within titles or text objects are handled differently on Windows and Mac If you include tabs within text objects the spacing of that text may change a lot when you open it on the other platform 4 Getting started with GraphPad Prism 1995 2014 GraphPad Software Inc s GraphPad Prism User Guide Prism is designed so you can just plunge in and use it But you ll master Prism more quickly if you check out the tips listed here and the guided examples of data analysis 1995 2014 GraphPad Software Inc Getting started with GraphPad Prism 47 4 1 A brief tour of Prism This five minute tutorial will show you a bit about how Prism is organized 1 When you start Prism you ll see the Welcome dialog You ll see six tabs representing the six kinds of data tables Click on the Column tab Then choose to use sample data for an unpaired t test Column tables have one grouping vari
40. 2 5 be rounded up to 3 or rounded down to 2 Both are equally accurate and many strategies have been proposed to deal with this issue The Wikipedia article on rounding explains the many possibilities Entering numbers into computers adds another layer of complexity Computers store the number as binary digits so need to convert to and from decimal For many values this requires rounding as well For example let s say you type in the number 0 055 and ask Prism to display the value to only two decimal places The next third digit is 5 One common rule to always round up when the next digit is 5 so you d expect Prism to display 0 06 But the computer 1995 2014 GraphPad Software Inc 146 GraphPad Prism User Guide can t store the value 0 055 Instead all values are converted to binary so this value is stored as 0 05499996 When rounding this value to two decimal places the next third digit is a 4 So Prism Windows rounds down and displays 0 05 Prism Mac rounds up in this case and displays 0 06 How Prism rounds By default Prism tries to show all the digits you entered and increases the number of digits after the decimal place to accommodate the extra digits But you can use the Format Numbers dialog to show fewer digits And the results of analyses can be rounded as well How Prism rounds values can seem erratic Prism rounds values that end with 5 somewhat unpredictably For example 0 25 gets rounded up to 0 3 but
41. 5 7 179 22 4 4 4 16 Control vs Treated Artagonst 4467 48 17 3 500 5091 6 6 0 6875 22 na no E 42 o 47 Control vs Treated Agonist 4467 61 40 16 73 5339 6 5 3134 22 18 Control vs Solvent Blank 4467 46 40 1733 15 339 5 0 3246 22 19 k A 4 4 4 L The results are shown here as tables In fact they will be tab delimited text or comma delimeted if that is set in the OpenOutput command Example 1 WBlock 7 6 4 PSummary WBlock 7 6 3 Significant 1995 2014 GraphPad Software Inc The results will be as shown below Here it is a table In fact it will be tab delimited text The delimeter is set in the OpenOutput script command and defaults to tabs Psummary Psummary Psummary Psummary Significant Significant Significant Significant Example 2 KKK ns ns Yes No Yes No mm S tw fl w we WBlock 7 6 4 PSummary WBlock 7 6 3 Significant The results will be as shown below Note the semicolon after the labels so in both cases the label and the columnID column run together PsummaryB PsummaryC PsummaryD PsummaryE Significant B Significant C Significant D Significant E Example 3 kkkk ns ns Yes No Yes No WBlock 7 7 4 PSummary WBlock 7 7 3 Significant Here there is no semicolon so the labels have their own column Psummary Treated say Psummary Treated Antagonist ns Psummary Treate
42. E E E Analyzing data with Prism How to analyze data With Pris cccecccsceceeeeeeeeeeeeeeeeeeeeeeeeeeeeneeeeseeeeseeeeeeeneeseeeeeeneeenanes 318 Creating chains of analyse Siiccciseccccsseed ceceiwec sees dieve dececuecttenseecdecetwecaceesiies Cosececeteessecseceawesexees 320 Changing an analysis sirontaa anede o ANa ao alean EA ATE aa eani a aana 321 Re peating an analysis sisciisicovccesasecsttecenbeciets euceutcneewnca ewe einan iaaiiai ianiai anes 322 Frozen and orphaned analysis reSults ccceeeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeneneeeeeees 322 Excluding data points from an amalySiS cccceeececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeesaeeeeeesaneeeeesaneeeees 323 Embedding results ona Qraph ccc ccciiecciseccteanatis eecdweccnsente drainn iarainn irria areen diniinan aii 325 Hooking to analysis and info COMStANES cccceeeeceee eee ee eeee ee eeeeeeeeeeesaeeeeeesaneeeeesaeeeeeesaneeeees 326 Simulating data and Monte Carlo simulations 335 Simulating a data table io einai e Eae ena a eceucteecetuadsetecdennsseuuecsscetuctersetues 336 How to Monte Carlo amalySes cccceseccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeaeeeeeesaeeeeeesaeeeeessaeeeeessaneeeees 337 Monte Carlo example Accuracy of confidence intervals ccccccceeeeeeeeeeeeeeeeeeeeeeeeeneeeees 339 Using a script to simulate many data Sets cccceeeeeeeeee ee ee ee eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeneneeeenes 342 How Prism generates rando
43. Error Bars Direction Fant Geek Error Bars Thickness Show Row Title Apply Dota Set Format For example on the graph below each data point is formatted to show different symbols and error bars directions for alternating data points 0 5 10 15 20 25 Format a range of data from the data table Select a block of data right click and choose Format Points 1995 2014 GraphPad Software Inc 206 GraphPad Prism User Guide Group A Group B Groupe Contro t A Y2 AY B Y1 C 2 c 3 D Y1 Cut Cti X Copy CtrieC Paste CtreV Paste Transpose Ctrl Shift T Paste Special Cirle Shifte V import Data Insert Delete Exclude Values Ctri E All Linked Highlight Points lt seperimposed semte gt gt 5 Tea gt Decimal Format grouped scatter Symbol Shape Column Width Symbol Size gt One More Subcolumn Border Color gt Data Object gt Border Thickness o Select Error Bars Color Use Larger Font CtrleM Error Bars Style gt Use Smaller Font Ctried Error Bars Direction Error Bars Thickness Show Row Titles Hide Row Titles Apply Data Set Format Revert individual formatting back to data set format Open the Format Graph dialog by double clicking on the graph Go to the Graph Settings tab and check the option to Remove all individual formatting 1995 2014 GraphPad Software Inc Prism Graphs the basics 207 F Format Graph
44. Example Your data source has thirty values in a single column and you wish to import into a Prism data table formatted for entry of triplicate Y values The first three values in the source data are the first three replicates The next three values in the source are the next set of replicates so they belong in row 2 of data set A After filling five rows you want to start inserting data into data set B Choose to import by rows placing three values on each row and starting a new column after five rows 1995 2014 GraphPad Software Inc Importing and exporting data 179 Row and column arrangement p Maintain row and column arrangement of the data source Transpose Each row becomes a column Byrows Place 3 values on each row VJAfter 5 rows start a new column By columns Stack values in each column ee ee ee ee ee ee ee ee Te ee E ee If the data source has the values from 1 to 30 in order Prism will organize the data as shown below When placing values side by side Prism does not pay attention to the difference between subcolumns and data sets It just puts values in the next cell to the right and it doesn t care whether that cell is another replicate a SD or the beginning of a new data set In the example above Prism placed three values side by side because you entered 3 into the dialog The data table was formatted separately for triplicate values ee ee ee eee ae ee eee ee e
45. Graph dialog apply to all data sets on the graph An alternative approach is to double click anywhere on the graph to bring up the Format Graph dialog Then click the All button if you want all changes to apply to all data sets If you don t do this changes apply only to one data set so you can plot some data sets one way and other data sets another way 11 4 Replicates and error bars on Grouped graphs Setting up data tables for entry of replicates or error values When you create a Grouped table choices on the Welcome or New Table dialog let you specify side by side subcolumns for entry of replicates or subcolumns for entry of error values computed elsewhere Learn more about Grouped tables Note an important 1995 2014 GraphPad Software Inc Error bars and replicates 151 distinction With XY and Grouped tables replicates are entered into side by side subcolumns with Column data replicates are stacked into columns The example below is set for entry of three replicate values triplicates but you can choose any number from 2 to 52 Y subcolumns for replicates or error bars Enter and plot a single Y value for each point Enter 3 replicate values in side by side subcolu Enter a Mean ed elsewhere Mean with SD Enter Mean with SEM Mean with 95 Cl Avail Mean with range Geometric mean Two wa Geometric mean with 95 CI Repeate Median Bonferre Median with range Organization of data tab
46. Guide 16 1 How to analyze data with Prism What analyze means in Prism Prism uses the term analyze to include not only statistics and regression but also for data manipulations such as transforming removing baselines and normalizing Step 1 Analyze dialog Start from any data table or graph and click the Analyze button There is no need to first select a range of data to analyze Prism completely ignores any selection you made before clicking the Analyze button Snalyze The analyze dialog appears Make sure the drop down on the upper left is set to Built in analysis and choose an analysis The right half lets you choose to only analyze selected data sets It is not possible to choose a subset of rows to analyze Prism always analyzes them all g Analyze Data ma Built in analysis hd Which analysis Analyze which data sets 3 Transform Normalize a J AUpbcal Der Transfoem Nommalize Prune rows Remove baseline and column math y Transpose x and Y 3 XY analyses Noriinear regression curve fit y Lines regression Fit spine LOWESS z BF differentiat ink a r When you analyze tables or graphs wth more SMON Galerenbale oF imegale Curve than one data set use this space to select Area under curve which data set s to analyze Deming Model II linear regression H Column statshes Row means with SD SEM Correlation Interpolate a Standard Curve Column analyses Grouped analyses C
47. K Y squared YAK log Y 1 log Y In Y 10 Y exp Y 1 Y sqrt Y logit y probit Y rank Y zscore Y sin Y cos Y tan Y arcsin Y ABS Y Y X lt x Comments Enter K in the box provided uv w Enter K in the box provided Log base 10 Natural logarithm base e Ten to the yth power inverse of log eY inverse of In Square root In Y 1 Y Y must be between 0 0 and 1 0 See notes below Column rank Smallest Y value gets rank of 1 Number of SDs from the column mean Y is in radians w AA Result is in radians Absolute value Gaussian Mean 0 SD K you enter Enter K in the box provided 1995 2014 GraphPad Software Inc Transforming normalizing etc s Many of the functions include the variable K Enter a value for K on the dialog When transforming Y values you can enter one value of K for all data sets or a separate value of K for each data set To enter different K values for each data set choose a data set enter K choose another data set enter its K and so on Rather than entering the value of K you can hook an analysis or info constant Notes about the probit function Prism uses an older definition of probit that adds 5 to all results to avoid use of negative numbers No it doesn t really make sense but this was once a common standard So probit 0 025 3 04 which is 1 96 5 00 probit 975 6 96 1 96 5 00 and probit 0 5 5 00 0
48. LabArchives server LabArchives usually uses a server maintained by LabArchives If you want to use a local server to host LabArchives files you can do so Details here 25 Support and license 1995 2014 GraphPad Software Inc as GraphPad Prism User Guide Prism makes it easy to get the support you need This section tells you about the Prism license agreement and how to contact our Support department 1995 2014 GraphPad Software Inc Support and license as 25 1 System Requirements Prism 6 for Windows runs under either the 32 or 64 bit versions of Windows 2000 XP Vista or Windows 7 but does not run under Windows 3 1 95 98 or Windows NT Prism will run in a screen as small as 800 x 576 Windows 8 and 8 1 come in four versions Prism runs fine as a desktop application on the pro and enterprise editions the successors to Windows 7 However Prism does not run on Windows 8 or 8 1 RT tablet computers or Windows 8 phones Prism 6 for Macintosh is a Universal application that runs on Intel and PowerPC based Mac computers using OS X 10 4 Tiger 10 5 Leopard 10 6 Snow Leopard 10 7 Lion 10 8 Mountain Lion or 10 9 Mavericks Prism requires 60 megabytes of space on the hard drive 25 2 Command line switches Windows only When Prism starts up you can give it some special instructions in the command line In order to add command line instructions edit the Prism exe start icon Right cli
49. Mac OS X Then choose About Prism It is more important to explain which analysis choices you made than which program you used For example it doesn t really help to say you fit a curve with Prism if you don t say which equation you selected how you chose to weight data points whether you fixed any parameters to constant values etc Citing a page in the user s guide Include the name of the page the date you accessed it and the URL Use this example as a guide What you can conclude when two error bars overlap or don t GraphPad Software Inc Accessed 5 November 2008 _ http www graphpad com faq viewfaq cfm faq 1362 1995 2014 GraphPad Software Inc s2 GraphPad Prism User Guide Citing the QuickCalc free web calculator Include the name of the calculator and the date you used it Here is an example Confidence intervals of proportions were calculated using the GraphPad QuickCalcs Web site http www graphpad com quickcalcs Confintervall cfm accessed November 2011 25 5 GraphPad Prism license agreement PLEASE READ CAREFULLY GRAPHPAD SOFTWARE INC GRAPHPAD IS WILLING TO LICENSE THE SOFTWARE IDENTIFIED ABOVE ONLY UPON THE CONDITION THAT YOU ACCEPT ALL OF THE TERMS CONTAINED IN THIS SOFTWARE LICENSE AGREEMENT THE AGREEMENT BY SELECTING THE I ACCEPT BUTTON BELOW OR BY INSTALLING UPLOADING ACCESSING OR OTHERWISE USING ALL OR ANY PORTION OF THE SOFTWARE YOU AGREE TO BE LEGALLY BOUND BY THIS A
50. Minor giid None X Color ks X Color mits x Thickness 1 pl Thickness 1 2 pt Style Style Use this dialog to set the origin of your graph and to format the color and shape of the axes or surrounding frame N b HAr To change the gap of an offset axis click and drag the end of the axis To draw a box around a graph including titles and numbering use the drawing tool Or wait until you assign a graph to a layout and choose the border on the second tab of that dialog 1995 2014 GraphPad Software Inc Graphs Frame and axes 15 1 3 Showing grid lines Regular grid lines Double click on the graph origin to open the Frame and Origin tab of the Format Axes dialog Or click on the Format Axis tool in the Prism toolbar Change P it a al amp ref K dh ule amp Fearr Axes Frame and Origin X avis Left Y axis Aight Y ais Tiles amp Fonts Origin Set ongin Automaticaly X Y intersects the X ads atX 0 0 X ntersects the Y aasatY 0 0 Shape Size and Position Size Wide X Distance of Y axis from left edge Width Length of X axis 3 00 in Distance of X axis from bottom edge Height Length of Y eas 200 in Axes and Colors Thickness of axes Color of plotting area Color of anes Page background Frame and Grid Line 1995 2014 GraphPad Software Inc 275 GraphPad Prism User Guide Special grid lines Double click an axis and use the Format Axis
51. Preferences dialog you can choose to export values using a period point or a comma as the decimal separator If you choose a period the US standard then adjacent columns are indeed separated by commas If you choose a comma then adjacent columns or subcolumns are separated by semicolons This is a very standard format useful for moving blocks of data into spreadsheet or word processing programs like Excel and Word When Prism exports into CSV it doesn t distinguish row titles X columns Y columns and subcolumns All the values are simply exported Special characters Greek subscripts etc are lost from column and row titles TXT This format is very similar to CSV except that adjacent columns are separated with tabs These are common formats and can be used to easily move blocks of data into spreadsheet or word processing programs like Excel and Word 1995 2014 GraphPad Software Inc GraphPad Prism User Guide This is a very standard format useful for moving blocks of data into spreadsheet or word processing programs like Excel and Word When Prism exports into TXT it doesn t distinguish row titles X columns Y columns and subcolumns All the values are simply exported Special characters Greek subscripts etc are lost from column and row titles XML When you export in XML format the exported file includes all special formatting including Greek characters subscript superscript subcolumn formats etc When
52. Prism as you can then check that nothing is too small One guideline from Cadmus who handles production for many journals is to make no font be smaller than 6pt and no line be thinner than 1 2 point What happens when you resize exported images EPS PDF WMF EMF files The EPS PDF WMF and EMF formats are all based on vectors and fonts These formats essentially store the instructions to draw the graph You can stretch them to any size and they should still look great The only exception is if you 1995 2014 GraphPad Software Inc 304 GraphPad Prism User Guide 21 8 pasted a picture onto your graph Then that picture will remain a bit map in your EPS etc file and may not look great if its size is changed Even though it shouldn t matter it is not a good idea to create an oversize graph and expect the journal to reduce the graph size and thus increase its resolution for TIFF files Journals prefer that you export the graph at the size it will be published TIF PNG JPG files TIF PNG and JPG files encode bitmaps If you stretch or shrink these images in another program that program has to figure out how to create extra pixels or remove existing ones Often the image becomes a bit blurry It is much much better to resize in Prism in the Graphs section and then export the bitmap image file at exactly the size you want it to end up at If you want to know the size of an image beware of viewing it after impo
53. Ri to 0 0003 AS First sort rows by X value Then average every K rows to produce one output row erage e New Graph Create a new graph of the results Lean Cancel Note that Prism can also decimate while importing data import a row skip K rows you enter K then import another row 1995 2014 GraphPad Software Inc Transforming normalizing etc 357 18 7 Fraction Of Total A Parameters Fraction of Total Divide each value by its Column total Row total Grand total Display results as Fractions D Percentages Confidence intervals E Calculate 95 00 confidence intervals Confidence intervals assume binomial data that each entered value is actual number of objects or events not normalized in any way Learn Cancel The fraction of total analysis divides each value by its column or row total or by the grand total This analysis is most often used for parts of whole data or for contingency tables but it can be used for column data and for XY or Grouped data tables so long as they have no subcolumns The calculation of confidence intervals only makes sense when each value entered into the table is an integer that represents the actual number of objects or events counted In this situation computing a confidence interval based on the binomial distribution makes sense Don t check the option to compute confidence intervals if the data are mea
54. Then press Delete When you delete a data table you have the option to delete all info results and graph sheets linked to the selected data tables at the same time 8 5 Emailing Prism files to colleagues Email Sheet pdf Email Family pzf Email Project pzf gt m n Click on the Send by Email button in the Send section of the Prism toolbar You can choose to send a Sheet Family or Project Your email program will open and create a new message with the Prism file attached The format of the file depends on what you choose e If you choose to send a data table or results sheet it will be sent as a text file e If you send a graph or layout Prism will send it as a PDF file e If you choose to send a family or project Prism creates a temporary copy of the project and attaches that to the email Changes you make after choosing the Send Mail command will not be included in the email even if you delay sending it These commands probably won t work if you use a web based email system or a nonstandard email program If the command doesn t work or isn t available you can still attach Prism files to email Simply save the file and then attach it to an email from your email program If you only want to send a subset of your project save the current sheet and all related sheets using the Save Family As command Choose Save Special from the File section of the Prism toolbar 1995 2014 GraphPad Software Inc
55. To import data into Prism from a text ASCII file Start from a data table and move insertion point to the cell in the data table that will become the upper left corner of the imported data Click on the Import button on the Prism toolbar Import x XML Prism will show you the Import and Paste Special dialog which will let you choose whether to embed or link to the original file Windows only and also will let you filter and rearrange the data as you bring it into Prism Note that it is not sufficient that a file have an extension file type such as txt 1995 2014 GraphPad Software Inc Importing and exporting data 171 or dat The file has to be a plain text file If a file is not a text file renaming it to have a different extension won t help 12 8 Importing and pasting choices The Import and Paste Special Choices dialog comes up when you import a file into a Prism data table or use the Paste Special command It has five tabs Source The Source tab lets you choose between importing or pasting just the values linking to a file or embedding a data object View The View tab lets you see the contents of the imported or pasted file divided into columns Filter The Filter tab let you choose which portions of the data file to import Placement The Placement tab lets you rearrange your data as you import paste it into Prism Info amp Notes The Info amp Notes tab gives you tools to import sections of a t
56. Upper lef corner of page Cancel OK 19 6 Creating a depth chart A depth chart is an XY plot rotated so the independent X variable is shown on the vertical axis and the dependent Y variable is shown on the horizontal axis This makes sense when the X variable is depth Follow these steps 1 Enter data on an XY table Enter the depth values into the X column 1995 2014 GraphPad Software Inc Page layouts 367 2 Prism will create an XY graph with X on the horizontal axis 3 Use the Format Axis dialog to change the direction of the numbering on both axes Set the X axis numbering to Below vertical Set the Y axis numbering to Left vertical 4 Delete the automatic X axis title because it cannot be rotated 5 Create an independent text object with the depth title Select it and rotate 180 degrees by clicking the rotate button in the lower right of the Text area in the toolbar several times Your graph will now look like this 8 g EIF 2 f s1 w ul y zd q 6 Assign that graph to a layout 7 Double click on the graph to bring up the Place graph on layout dialog Go to the second Size and Location tab and choose to rotate 90 degrees clockwise 1995 2014 GraphPad Software Inc ses GraphPad Prism User Guide Assign Graph Sie and Locaton Hint You can diag and stretch graphs and placeholders on the layout tsef so the choices below are only needed in special situations Scaling Factor
57. When you enter new data Prism will update the analyses and graphs To delete a block of data completely select Delete from the Edit menu Other data on the table will move to fill the gap e Shift space selects the entire row Windows 1995 2014 GraphPad Software Inc Data tables 143 e Control space selects the entire data set Windows e Control A selects the entire table Windows e Shift Control Space selects the entire row Mac e Shift Option Space selects the entire data set Mac e Command A selects the entire table Mac 10 14 Inserting a series Often you ll want your X column of an XY table to be a regular series of values Prism offers two ways to do this Using the Insert Series command Follow these steps to insert an arithmetic or geometric series 1 Place your insertion point in the first cell of the series Alternatively select the entire range that you want to contain the series 2 Drop the Insert menu and choose Create Series Or click the corresponding button in the Change portion of the toolbar Create Series Create series with 10 values atanged vertically First value 1 0 Change Calculate each value on H X Eo i 3 Enter the number of values you intend the series to have If you preselected a range of values Prism will default to the number of rows in that range Also enter the first value and the rule to increment other values Valua just above t plu
58. You must enter X error values directly Prism cannot compute them You can only enter one value for X errors SO X error bars are always symmetrical Entering multiple sets of data that don t share X values Each data table has a single column for X and up to 104 sets of Y values What should you do if you have different X values for each set of Y values There are two ways to solve this problem The best approach is to stagger the data entry You don t have to start entering data in the first row This example shows three data sets with different X values Takin cae X Group Group B Group C Gror XY d E X Y Y i 1 1 1 2 2 3 3 4 1 1 5 21 5 6 3 1 7 1 8 2 8 9 33 Qo 11 An alternative approach is to enter each data set on a different table The disadvantage with this method is that you lose some analysis choices You must enter all the data sets on one table in order for Prism to compare linear regression lines to compare best fit values from nonlinear regression and to compare survival curves Another minor disadvantage is that Prism will automatically make a different graph for each table However you can delete the unneeded graphs and include data from all the data tables on a single graph 1995 2014 GraphPad Software Inc Distinguishing the six kinds of data tables 115 9 4 Column tables one grouping variable In a column data table each column defines a group These groups are
59. answer 1000 So the logarithm of 1000 is 3 If you multiply 10 by itself 3 times you get 1000 You can take 10 to a negative power For example taking 10 to the 3 power is the same as taking the reciprocal of 10 So 10 equals 1 103 or 0 001 The 1995 2014 GraphPad Software Inc Graphs Frame and axes 315 logarithm of 0 001 is the power of 10 that equals 0 001 which is 3 You can take 10 to a fractional power Ten to the 1 2 power equals the square root of 10 which is 3 163 So the logarithm of 3 163 is 0 5 Ten to the zero power equals 1 so the logarithm of 1 0 is 0 0 You can take the logarithm of any positive number The logarithm of values between zero and one are negative the logarithms of values greater than one are positive The logarithms of zero and all negative numbers are undefined there is no power of 10 that gives a negative number or zero Logarithms to other bases The logarithms shown in the previous section are called base 10 logarithms because the computations take 10 to some power These are also called common logarithms You can compute logarithms for any power Mathematicians prefer natural logarithms using base e 2 7183 Despite that name use of logarithms with base e does not seem natural to most scientists who tend to be far more comfortable with base 10 logarithms Biologists sometimes use base 2 logarithms often without realizing it The base 2 logarithm is the number of doubling
60. area defined by the axes Both can be set by right clicking control click for mac on the graph or by dropping the color wheel icon Layouts of course only have the page background property Which export formats allow you to choose a clear background With Prism Windows you can choose a clear background when you export in PDF EMF or WMF formats Prism Windows cannot export TIFF or EPS images with clear backgrounds but Prism Mac can With Prism Mac you can choose a clear background when you export to PDF TIFF and EPS format This choice is in the Exporting options part of the Export Graph dialog where you can choose to include a background color or export with a clear background Copying graphs and layouts to the clipboard Choose on the File amp Printer tab of Preferences whether you want Prism to copy graphs and layouts to the clipboard with the background color you specified in Prism or with a clear background 1995 2014 GraphPad Software Inc 3 GraphPad Prism User Guide Info Sheet Send to MS Office File amp Printer New Graphs Analysis Intennet Automatic backup Every time a different sheet is viewed WlEvey 5 minutes F Allow recovery of unsaved files from the Welcome dialog File Format D PZF PZFX Cannot be opened by Prism 4 but data and info are in XML format that other programs can access F Do not save or read page size to or from pzf file Save compact
61. baseline divide by the baseline compute the fractional or percentage difference etc Note that you can also use this analysis to add or multiply two columns 18 4 Normalize Normalize the data to convert Y values from different data sets to a common scale This is useful when the want to compare the shape or position EC50 of two or more curves and don t want to be distracted by different maximum and minimum values Investigators who analyze dose response curves commonly normalize the data so all curves begin at 0 and plateau at 100 If you then fit a sigmoidal dose response curve to the normalized data be sure to set the top and bottom plateaus to constant values If you ve defined the top and bottom of the curves by normalizing you shouldn t ask Prism to fit those parameters To normalize click Analyze and choose Built in analyses Then select Normalize from the list of data manipulations to bring up this dialog 1995 2014 GraphPad Software Inc 354 GraphPad Prism User Guide E Parameters Normalize How is 0 defined Smallest value in each data set First value in each date set or last whichever is smaller mm the Ye becomes 0 for all data sets How is 100 defined Largest value in each data set Last value in each data set or hrst whichever is larges oo the Y T becomes 100 fo all data sets The sum of all values in the data set column Present results as Fractions Percenta
62. begin a new project you ll see the Welco me dialog New table amp graph anes Most of the time especially when new to Prism you ll use one of Ss the six tabs on top to create a new table and graph Survival Parts of whole Open a file Open a file LabArchives Click on a folder or file to open it Or click on Desktop and other folders to browse all your files Clone a graph Graph portfolio After you have used Prism a bit you may see files listed under the heading Unsaved Files How can you open a file that wasn t saved When you exit Prism as with any program it asks you whether you want to save changes to every open file If you click No Prism still saves the file in a special location for four days and shows it in the list of unsaved files LabArchives LabArchives is an innovative web based product that enables researchers to store organize and publish their research data Far more than an ELN Electronic Laboratory Notebook LabArchives stores and catalogs all of your research for easy retrieval and publication You can save files to LabArchives from Prism And you can open Prism files saved on LabArchives from the Welcome dialog without going to www labarchives com Clone a graph Cloning a graph is making a copy of it along with the data table and any linked analyses At the time you clone a graph Prism will give you the option of deleting the data Add your own data and your done From the We
63. choose to paste link or paste embed Numbers a Mac spreadsheet that is part of iWork does not copy the HTML so pasting from Numbers always uses the older style Two ways to paste from the HTML older Excel versions only It gets even more complicated The HTML clipboard version from some versions of Excel contains each number twice One copy shows exactly what you see in Excel The other copy shows the value with more decimal places ignoring formatting or rounding within Excel By default Prism pastes the values as they are shown in Excel But the Paste Special dialog lets you use the other version if you prefer x Paste as many digits as possible If Excel rounds to 1 23 paste 1 23456 This option is not available if you copy from Excel Windows 2007 or later as the necessary information is not copied to the clipboard Importing data from text files Rather than copying and pasting via the clipboard you can transfer data from Excel or other applications to Prism using text files This is most useful if you need to move data from Excel running on one computer to Prism running on another To create a text file from an Excel spreadsheet Go to the worksheet tab you want to export then pull down Excel s File menu and choose Save as Select either Text tab delimited or CSV comma delimited format To import a TXT or CSV file into Prism 1995 2014 GraphPad Software Inc Importing and exporting data 169 Start
64. clarify what they mean Previous versions of Prism and some other programs used the term embed to describe converting fonts to outlines Adobe and some journals use the term embed to the describe the third approach above an approach that Prism does not offer Choosing a color model If your graph is entirely black on white choose the monochrome or gray scale color model If your graph includes color choose the color model requested by your journal Different journal have different requirements It seems that RGB is now more popular than CMYK so choose RGB if your journal has not specified Previewing EPS files Once you ve exported an EPS file from Prism you ll probably want to see it to 1995 2014 GraphPad Software Inc Exporting images from Prism 301 make sure it is correct With Macs this is no problem Just double click on the file and it will be opened in Preview a program that is part of the OSX system What actually happens is that Preview converts from EPS to PDF and displays the pdf image Windows however has no built in program that can view EPS files Adobe Illustrator seems to be the standard that many journals use so import the EPS files into Illustrator if you can If you don t have access to Illustrator you ll have to find another program Try double clicking on the file to see if you already have a program that can open EPS files Also try the free program GhostScript which works OK Another opti
65. confidence intervals and then transform both ends of the confidence interval The resulting 95 CI will be asymmetrical Transforms for pharmacology and biochemistry Eadie Hofstee Hanes Woolf and Lineweaver Burk transforms are used to plot enzyme kinetic results Scatchard transforms are used to display radioligand binding and Hill plots are used to plot dose response data 1995 2014 GraphPad Software Inc 350 GraphPad Prism User Guide Important Use these transforms only as a way to display data not as a first step in analyzing data You ll get better results by using nonlinear regression on the actual data Here is the mathematical definition of each transform Function X becomes Y becomes Eadie Y X No change Hofstee Hanes Woolf No change X Y Hill No change if you log10 Y Ymax Y entered your Prism prompts for data as Y max log conc Log10 X if you entered your data as concentration Lineweaver 1 X 1 Y Burk Log log Log10 X Log1i0 Y Scatchard Y Y X Prism can also create Bland Altman plots which require a simple transform of the data However this is not done via a transform but rather via a separate analysis User defined transforms When writing your transform you may use any of these functions when writing your equation Mostly functions are pretty standard Beware of the sqr function which has different meanings in different environments In Prism sqr squares the value
66. continue to the next statement in the Visual Basic program or macro It will NOT wait for Prism to complete before continuing If you don t take the extra steps described below your Visual Basic program will try to read a file containing Prism s results before Prism has finished creating that file To avoid this make your Visual Basic program pause until Prism creates a file When you write the Prism script include lines at the end of the script to create a file that will tell Visual Basic you are done The example below creates done txt 1995 2014 GraphPad Software Inc a GraphPad Prism User Guide OpenOutput done txt WText done CloseOutput Your Visual Basic code should first delete the file done txt if it exists from a previous run and then launch Prism Immediately following include these lines that make your program loop until done txt is created Do Until Dir HD prism 5 done txt gt Application Wait Now TimeValue 00 00 1 Loop The first line in the example above checks whether the file done txt exists Change the path and file name as needed If the file exists Prism is done Visual Basic continues beyond the loop with any code that follows If the file doesn t exist yet Visual Basic waits 1 second and then loops back to test again whether the file exists MacScript tell application HD Prism4 Prism Chr 13 _ quit Chr 13 _ end tell Run a script fro
67. data sets on the graph Click the Global button to select all data sets on the graph Or select the data sets from the drop down menu that you want to change If your graph only has one data set one slice The graph is generated from values entered into a single column in the data table If you enter data into a row you ll only get one value on the graph Color and Legends You can set the color of each graph segment Use the roll down to choose if you want a particular segment of a pie or donut graph exploded from the main graph and how far away you want it to be Or choose to hide a segment Format Graph Ieee Graph type OO madi Colors amp Legends Male vjs gt Global Color a Sice Show legend left to night Applicants for admission in 2011 am 55 43 567 Female Women 1023 Men Students Choose the information you want the legend to show and how you want it formatted Y Show legend left to nght J Color V Percentage Vake V Label 1995 2014 GraphPad Software Inc 268 GraphPad Prism User Guide If one of the rows of data is zero then Prism will not create a legend for it If you want a legend even though the value is zero enter some tiny nonzero value like 0 000001 The slice will be invisible on the graph but Prism will create a legend for it Borders Choose the color and thickness of the segment borders You can have different settings for the inner
68. data table column widths To adjust the width of a column click anywhere on a column border and drag If you first select several columns dragging the border of one column will change the width of all selected columns Prism determines the width of subcolumns replicates automatically and you cannot change these widths individually To make all larger or smaller resize the main column x 1995 2014 GraphPad Software Inc 138 GraphPad Prism User Guide 10 10 Specifying decimal places in a data table Decimal format Prism automatically chooses the number of decimal points to display in a data table automatically To change the number of decimal points displayed Select the column or columns you wish to change click at the top of the column to highlight and click on the Change decimal format button of the Change toolbar Change aX O Notes e When you place the insertion point click the mouse cursor in a particular cell in a data table Prism expands that value to show all digits When you move to another cell the value reverts back to the selected numerical format e It is not possible to change decimal format of a contingency table or the Y values in survival tables since all values must be integers e You can only change numerical format for an entire column or several columns It is not possible to change the numerical format of individual cells Decimal separator In some parts of the world
69. defined by one scheme perhaps control vs treated You can have more than two groups in a one way table for example placebo vs low dose vs high dose Analyses performed with Column data e t test one sample paired and unpaired e Mann Whitney Wilcoxon Column statistics including normality tests One way ANOVA followed by Tukey Dunnett Newman Keuls or Bonferroni post tests Kruskal Wallis Friedman Bland Altman ROC curves Example of a column table Table format GfoupA GroupB GroupC Gro Control Drug A i Drug B Y T 1 31 98 2 61 90 3 31 8 4 43 77 5 5 71 6 34 7 7 n e Each column defines a treatment group Prism does not use a separate column to enter the grouping variable Instead the groups are defined by columns e If data are not matched or paired rows have no special meaning Enter data in any order you like e If data are froma before after experiment with clear pairing or matching place each set of matched results on one row Optionally use the row title to label it Blue italics values are excluded ignored by analyses and graphs Use Exclude Values Error bars For one way tables Prism will calculate error values and create error bars automatically Enter all the values for a data set in a single column 1995 2014 GraphPad Software Inc ne GraphPad Prism User Guide Group A Group B Group C Gro Drug A Drug B T Y Table format Control vy Oo WO
70. dialog e To change the shape and size of a graph by stretching Click once on an axis to select it Then drag on either end to stretch e To make a graph proportionately larger or smaller Click Resize Graph 1995 2014 GraphPad Software Inc GraphPad Prism User Guide button on the Change section of the Prism toolbar Change Arrange Oraw Si LS l A aj vi Bit a OF 7 Smaller f Larger To Fill Page More Choices e To change the thickness or color of one axis Click once to select that axis Then click Change and choose Selected Object s If you change the X axis the top part of the axis frame will also change accordingly If you change the left Y axis the right part of the axis frame will also change accordingly unless you created a right Y axis e To move the graph and axis titles closer to or further from the graph Position the mouse near the title until the cursor becomes a two headed arrow Then drag e TO move the axis numbering or labeling closer to or further from the axis Move the mouse over the numbering until the cursor becomes a two headed arrow Then drag Or click once on the numbering to select Then nudge one pixel at a time by clicking the arrow keys e Double click on the origin of a graph to bring up the Frame and Origin tab of this dialog e To format the size font color etc of the numbering of an axis click to select the axis and then use the controls in the Text toolbar 15 1 Fr
71. dialog e Graph Portfolio to help you master Prism Click the Portfolio tab on the Welcome dialog to browse a portfolio of polished graphs Open any of these graphs to explore how it was made e Open files you forgot to save When you exit Prism as with any program it asks you whether you want to save changes to every open file Have you ever clicked No by accident and lost your work Not with Prism 6 You can open unsaved files from the Welcome dialog unless you tell Prism not to keep them or unless you waited more than three days Launch two instances of Prism When you open Prism Windows it is limited to use on one display If you open several projects each project is a window within the larger overall Prism window With Prism 6 you can launch a second copy of Prism with its own windows You can t launch the second instance from within Prism Instead double click on the program icon Open files directly from LabArchives From the Welcome dialog of Prism 6 you can open a file directly from LabArchives so don t need to first go to labarchives com to download the file you want With Prism 6 you can upload files directly to LabArchives introduced in Prism 5 04 and 5 0d Prism 6 but not Prism 5 also sends LabArchives a list of all words used in notes titles text boxes etc so you can search within LabArchives to find the file you need Easier to find the sample data sets Prism 5 introduced sample data sets as a way to lear
72. displaying only a Prism icon instead of the full graph or layout This won t be useful very often EMF or WMF Windows supports two similar formats for describing images using vectors and fonts The WMF Windows Metafile format is older The EMF Enhanced 1995 2014 GraphPad Software Inc Exporting images from Prism 403 metafile format is newer and in theory a bit better In fact one format works better for some programs and the other format for others It seems impossible to predict By default Prism places both formats on the clipboard and lets the pasting program decide which one to use Because some programs make the wrong choice we let you choose whether Prism copies EMF WMF or both Choose at the bottom of the File amp Printer tab of the preferences dialog If you re having problems with pasted graphs looking funny try setting another format as the default choice for copying and pasting Preferences Into err Locations Send to MS Office View Ae t Pass New Graphs Analysis Intenet Automatic backup J Every time o diferent sheet is viewed YiEvey 5 minutes File Format PZF m PZFX Cannot be opened by Prem 4 but data and nfo are in XML fomat that other programs can access Do not save or read page size to or from pef file Save compact smaler but requires recalculabons after opening J Always prompt when saving to a temporary folder Print Options s Print grid lines on tables
73. do you change the order in which data sets are plotted Change the order to determine plot lines are in front Plotting area matters the most when you use area fills The graphs below are the same but with the plotting order reversed Note that on the graph on the left the area fill from the one data set hides the other 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 263 Survival of Two groups Survival proportions Survival of Two groups Survival proportions 100 100 50 0 Or eee 600 1000 1500 2000 600 1000 160 2009 To change the plotting order of the data sets on a graph Click the Rotate Flip button in the Change section of the Prism toolbar to reverse the front to back order of data sets on a graph Change fi E ue K Wh nly amp To fine tune the front to back order go to the Data Sets on Graph tab of the Format Graph dialog 1995 2014 GraphPad Software Inc 264 GraphPad Prism User Guide g Format Graph Appearance Data Sets on Graph Graph Settings The order of data sets in this list determines what happens when two data points overlap Data sets placed higher on this kst wil be graphed in front of data sets lower on the list Data sets plotted front to back io of Thee groups Survival proportions A Coritrol Data on graph Tiree groups Survival proportions B Treatment _ a Three groups Survival propoitions C Treatment B
74. e Merge a copy of the graph along with its data tables and analyses into the project you are working on now The advantage of this approach is that everything will be in one project The disadvantage which some consider to be an advantage is that the data will now exist in two files Another advantage is that your file is self contained Even if you move it to a different computer everything will work Live link The data and graph are not in the project with the layout To edit a linked graph go to the original project Then resave that file and the changes will appear in the layout Prism can maintain the link only if the name and location of the linked file doesn t change If you change computers you ll almost certainly break the link The advantage of linking which some will consider to be a disadvantage is that the data and graph only exist in one place e Unlinked picture As the name suggests this is just a picture that is not linked to any data or any editable graph Cropping The first tab of the Assign Graph graph dialog lets you crop a graph to get rid of white space or portions of the graph you don t want to see on the layout If you enter a negative value for any of the cropping values you ll make the graph placeholder larger adding white space in that direction The second tab Size and Location lets you add a border around the graph and change its size and position 19 4 Adding another graph to the layout When y
75. example you can first transform data then normalize the transformed data then fit a curve to the normalized results and finally run a normality test on the residuals from the curve fit To make it easier to view analysis chains Prism can show an additional folder in the Navigator labeled 1995 2014 GraphPad Software Inc Data with Results F Mi Data with Results E Data 1 Fj Iransform of Data 1 lA pes Nonlin fit of Transform of Data 1 lA Table of results lA Curve Normalize of Transform of Data 1 Nonlin fit of Normalize of Transform of Data 1 LA Table of results LA Curve DE The default is to show the Data with Results folder whenever a results sheet is analyzed To change this default click on the Prism section of the Toolbar and select Preferences and then click this option in the View tab Use the Search tool Click Find from the Edit menu or click on the binoculars icon in the bottom toolbar or use the control F shortcut key to search for sheets in a project containing specific words or text The results will appear in the Search Results folder which you ll see in the Navigator Prism searches for the text you entered in titles floating notes sheet names and more It only searches within the current file and does not search within other files that might include the search text 1 gt EHDA Finel E Find ai sheets x including this exact phrase
76. fonts this format lets the journal producers edit the text or change the font and size The only drawback is that if the file is opened on a computer that does not have the exact fonts you used another font will be used and the look of the graph or layout will change If you use standard fonts we recommend this approach If you check the option to convert all text to outlines or glyphs the look of your graph or layout will be preserved on any computer even one that does not have the fonts you used The disadvantage is that the text no longer is encoded as text so the people processing your files at the journal will not be able to edit the text change the point size or switch to a different font We only recommend this approach if you use any unusual fonts in your figure and are not sure if the journal computers will contain those fonts Prism Mac always converts fonts to outlines Adobe products offer a third way to deal with fonts that combines the best of the two approaches above but Adobe has not provided the hooks our programmers would need to implement this approach If you have access to Adobe Illustrator here is an approach that is likely to work well Export the graphs from Prism Windows without converting the text to outlines Or try copy and paste Then export from Illustrator in EPS format We do not use Illustrator so can t give you any detailed information Beware of the term embedded font If your journal asks for that
77. formats that let you set resolution dots per inch enter 100 300 600 or 1200 You cannot enter other values The default is 300 dpi For tif or pdf export set the mode to RGBlow 256 colors RGBhi millions of colors CMYK default or MONO Note that MONO means black and 1995 2014 GraphPad Software Inc white only with no grays CMYK and RGB are two ways of denoting colors Publishers usually but not always prefer RGB For tif export include the compress option to save the file using PackBits compression which will make the file smaller but perhaps less compatible Or use the LZW option Windows only to compress using the Lempel Ziv Welch algorithm which doesn t compress quite as well as PackBits but may be more compatible with some programs For EPS export choose nofonts to not include fonts This makes the EPS file smaller and more compatible but requires that the same fonts be present on the computer used to import the file Set the mode to rgb cmyk or gray If your page has a colored background you will see that background in the exported file unless you include the parameter Clear to export the graph or layout with no background color only allowed for some formats For all export commands Prism will use the SetPath location if you don t specify disk and directory i Ifyou use F to export a file with the same name as the _ imported data table remember to ap
78. from a data table and move insertion point to the cell of the data table that will become the upper left corner of the imported data Click on the Import button on the Prism toolbar Import TX XML Prism will show you the Import and Paste Special dialog which will let you choose whether to embed or link to the original file Windows only and also will let you filter and rearrange the data as you bring it into Prism Note that you can t open a text file directly from Prism s Welcome dialog or with the File Open command To import a file you must first create a new Prism project or open an existing one go to a data table position the insertion point and then choose the Import command 12 7 Importing text and Excel files directly Importing Excel files To import data into Prism Windows only directly from an Excel XLS file Start from a data table and move insertion point to the cell that will become the upper left corner of the imported data Click on the Import button on the Prism toolbar Whenever possible transfer data from Excel using copy and paste Import TX XML Prism will show you the Import and Paste Special dialog which will let you choose whether to embed or link to the original file and also will let you filter and rearrange the data as you bring it into Prism Limitations to importing Excel files directly If your Excel workbook spreadsheet file has several worksheets tabs Prism only reads one
79. from raw data You enter a stack of values and Prism computes the range and percentiles to make the box and whiskers graph 1995 2014 GraphPad Software Inc 240 GraphPad Prism User Guide You need to be just a tiny bit sneaky if you want to enter the minimum 25th percentile median 75th percentile and maximum values directly Prism won t know that you entered those values but will make the graph as if you entered raw data If you just enter those five values Prism will correctly compute the minimum maximum and median but the 25th and 75th percentile values Prism computes will be incorrect Here is a trick Enter the median value three times rather than once and also enter the minimum maximum and 25th and 7th percentile values For each group enter seven values on separate rows of one column the order doesn t matter e Minimum 25th percentile Median Median Median 75th percentile e Maximum You can t tell Prism that these values are not the raw data so it thinks they are raw data and so computes the minimum maximum median and quartiles from those seven values and plots those computed values which exactly match the values you entered 14 2 6 Forest plots This graph below is a Forest plot also known as an odds ratio plot or a meta analysis plot It graphs odds ratios with 95 confidence intervals from several studies 1995 2014 GraphPad Software Inc Graphs Symbols bars lines
80. is not permitted under this Agreement then i you are liable to pay for any unpaid license fees as well as the reasonable costs of the audit and ii the license grant with respect to the Software will terminate immediately Any information obtained by GraphPad or GraphPad s authorized representative during the course of such inspection and audit will be used and disclosed by GraphPad solely for purposes of such inspection and audit and for enforcement of GraphPad s rights under this Agreement and applicable law unless other uses or disclosures are required under applicable law Nothing in this Section shall be deemed to limit any legal or equitable remedies available to GraphPad for violation of this Agreement or applicable law MANDATORY ACTIVATION Activation associates the use of the software with a specific computer During activation the software will send information about the software and the device to GraphPad This information includes the version the serial number the Internet protocol address of the device and information derived from the hardware configuration of the device BY USING THE SOFTWARE YOU CONSENT TO THE TRANSMISSION OF THIS INFORMATION UNLESS THE SOFTWARE IS ACTIVATED YOU HAVE NO RIGHT TO USE THE SOFTWARE This is to prevent its unlicensed use YOU ARE NOT PERMITTED TO BYPASS OR CIRCUMVENT ACTIVATION You must activate every computer from which Prism is used GENERAL RESTRICTIONS You agree and acknowledge that u
81. many times and tabulate the results Prism 6 makes this possible with a new Monte Carlo simulation analysis that makes it easy to tabulate the results of many simulations First simulate a data table and run an analysis to analyze that table Then run the new Monte Carlo analysis Specify how many simulations you want to run and which analysis parameters to tabulate You can also define a hit as perhaps a P value less than 0 05 or a confidence interval including a theoretical value The results of the Monte Carlo analysis include a table with all the tabulated data that you can analyze further and a table of the number of simulations that were hits 2 3 What s new Multiple comparisons e Multiplicity adjusted exact P values can be reported with Bonferroni Tukey Dunnett Dunn or Holm Sidak multiple comparisons testing following one or two way ANOVA An adjusted P value is an exact P value reported for each comparison but its value depends on the number of comparisons Tukey s multiple compansons test Mean 95 Cl of diff Significant Summary Adjusted P Value Treated vs Control 38 80 20 49 to 57 11 i a 0 0003 Treated Antagonist vs Control 600 15 71 to 20 91 0 9245 Treated Antagonist vs Treated 36 20 54 51 to 17 89 es _ 0 0005 e Fisher s unprotected Least Significant Difference LSD comparisons are a second approach to report exact P values following ANOVA This method does not co
82. need to specify the row column and subcolumn of the upper left corner of the data object you wish to import into Note that the ImportLink command updates a Prism data object linked to a text file IF you Paste Link data from Excel you cannot update the link using this command You d need to write VBA code in Excel to change the data in Excel 1995 2014 GraphPad Software Inc 4 GraphPad Prism User Guide 23 2 11 Importing data from the script file Commands InsertData lt row gt lt col gt lt subcol gt InsertDataLink lt row gt lt col gt lt subcol gt Explanation If you create the script file from within another program you can include data and info constants within the same file as the script commands The InsertData command imports data included within the script file into the current data table starting at the specified position The data are included right in the script file enclosed between the tags lt Data gt and lt Data gt The rest of the script continues right after the lt Data gt tag InsertData lt Data gt 1 2 4 5 7 9 lt Data gt The InsertDataLink command imports data included within the script file into a data object whose upper left position is at the indicated position This works similarly to the ImportLink command If you want to import starting at a particular row or column specify them Row O is the title row and row 1 is the first row with data Column 0 is the X c
83. of dots TIFF files tend to be trouble free when submitted to journals 1995 2014 GraphPad Software Inc Exporting images from Prism 387 You need to choose resolution color model and size The resolution is expressed as dots per inch dpi Computer screens display images at about 100 dpi Computer printers generally print at 300 600 dpi and publications are generally printed at 1200 dpi Journals typically ask for a file at 1200 dots per inch dpi the highest resolution that Prism offers Choose between two ways to express colors RGB designed for computer monitors or projectors or CMYK designed for printing If you are submitting to a journal follow their instructions If in doubt choose RGB You can also choose Monochrome files which are pure black and white with no grays If you choose RGB choose between 256 colors smaller files or millions of colors larger file but more accurate color rendition Typically graphs and layouts in Prism projects are much larger than publication size If you ask for a graph at 1200 dpi at the actual size in Prism you will end up with either a huge file or an out of memory error message Avoid this problem by specifying the publication size Let s say your graph is 6 inches wide but you will publish it with a width of 2 inches By checking the option to reduce the graph to a width of 2 inches you will create a file one ninth as large one third the width times one third the heig
84. or graph and click the Analyze button Don t overuse this New button Prism offers lots of ways to recycle to analyze and graph new data using the same steps and format that you used earlier 1995 2014 GraphPad Software Inc Getting started with GraphPad Prism s 4 7 Tips for using Prism Expand all tips Collapse all tips Getting started tips a Before using Prism for the first time If you are new to Prism start by reading this one page list of essential co Also consider arranging on site training Pay attention to the distinctions between the six kinds of data tables When you create a new data table choose between a XY Column Grouped Contingency Survival and Parts of a Whole table Understanding how these tables are used will make it much easier to use Prism effectively Grouped Contingency Survival Parts of whole Learn about the various approaches to making bar graphs Spending a few minutes reading about the various approaches to making bar graphs will prevent some aggravation later Bar graphs can be created from Colum Grouped XY or Contingency tables Recycle your work Once you ve analyzed data and made some graphs with Prism you ll probably want to do similar analyses and make similar graphs with new data Don t start again from scratch Prism offers four ways to recycle your work without programming You can duplicate a family clone a graph use the Wand to repeat analyses or s
85. placeholder so the graph itself would get smaller on the layout when you added a legend or text box or image to a graph e Enlarge or shrink an entire layout Enlarge or shrink an entire layout Prism 6 has a new toolto as well as enlarging or shrinking an entire graph which you could do in Prism 5 e Easier to place a graph from one project into the layout of another Prism 5 allowed you to link a graph from one project into a layout of another This lets you keep each project compact and avoids the need to put all the data and results for one layout in one file But that feature has been hard to discover and used an extra popup dialog Prism 6 makes it easier to discover and use by placing the choice on the first tab of the layout dialog e Draw elbow and zig zag lines e Place borders around graphs in layouts After assigning a graph to a layout you can crop it and or define a border 1995 2014 GraphPad Software Inc 34 GraphPad Prism User Guide e Thinner lines We ve added a new choice to make lines and curves of a point thick With Prism 5 the thinnest choice was 1 2 point You won t notice the difference on screen but you may notice the difference on printouts or high resolution exported files 2 13 What was new in Prism 5 In case you are upgrading from Prism 4 the pictures below show the biggest improvements in Prism 5 For details read this 16 page pdf document New users will love the
86. questions e It is difficult to describe graphing and analysis problems on the telephone When you email us a question you can attach your Prism files exported images or screenshots of error messages This helps us figure out the problem and provide helpful solutions 1995 2014 GraphPad Software Inc Support and license 461 e In many cases our answers contain screen shots or links to pages on our web site Trying to relay a URL via telephone doesn t work very well e We keep a record of problems and solutions When you receive a email from us you can always refer back to it even weeks or months later And we can keep a record of the questions you asked and whether or not we solved your problems We use these records to help others with similar questions and to help design new versions of our software e We often answer emails while traveling or from home This lets us answer much more promptly than we could by phone 25 4 How to cite Prism Citing Prism When citing analyses performed by the program include the name of the analysis and Prism version number including the second number after the decimal point Use this example as a guide One way ANOVA followed by Dunnett s multiple comparisons test was performed using GraphPad Prism version 6 00 for Windows GraphPad Software La Jolla California USA www graphpad com To find the full version number pull down the Help menu Windows or the Prism menu
87. recently used locations Send to MS Office tab e Set default formatting options when sending a file to Word Also select default for linking and embedding options for sending Prism objects to Office applications e Note that when sending files to PowerPoint and Word some combinations of operating system and Office version tend to like one format over another 1995 2014 GraphPad Software Inc 2 GraphPad Prism User Guide 7 Work efficiently Repeat analyses and graphing Once you ve analyzed data and made some graphs with Prism you ll probably want to do similar analyses and make similar graphs with new data Don t start again from scratch Prism offers four ways to recycle to quickly analyze and graph 1995 2014 GraphPad Software Inc Work efficiently Repeat analyses and graphing s new data using the same steps and format that you used earlier 7 1 Duplicate a family of sheets A family is defined to be a selected sheet and all linked sheets To duplicate a family of sheets do one of the following e Click the New button and choose Duplicate Family 1995 2014 GraphPad Software Inc o GraphPad Prism User Guide 7 2 e Drop the Insert menu and choose Duplicate Family e Right click or Control click if using a Mac on any sheet in the Navigator and choose Duplicate Family If you are starting from a data table Prism will ask you to assign a name to the new duplicated data table If th
88. recruit subjects as pairs matched for variables such as age ethnic group and disease severity One of the pair gets one treatment the other gets an altemative treatment You run a laboratory experiment several times each time with a control and treated preparation handled in parallel You measure a variable in twins or child parent pairs Matching should be determined by the experimental design and definitely should not be based on the variable you are comparing If you are comparing blood pressures in two groups it is OK to match based on age or postal code but it is not OK to match based on blood pressure Assume Gaussian distribution the assum Review analysis check lists I O nce yo u ve com pleted the The paired t test compares the means of two matched groups assuming that the distribution of the before after differences follows a Gaussian distribution analysis review the accompan in ana s is Are the differences distributed according to a Gaussian distribution 3 p y g analysis The paired t test assumes that you have sampled your pairs of values from a population checklist to co nfirm yo um ade of pairs where the difference between pairs follows a Gaussian distribution While this assumption is not too important with large samples it is important with small the rig ht cho ices sample sizes Test this assumption with Prism Note that the paired t test unlike the unpaired t test does n
89. subcol gt Explanation The Import command imports data from a text file into a data table The ImportLink command replaces data in a data object file using existing choices for filtering and rearranging If you omit the filename and are in a ForEach file loop Prism will use the current loop s file If you include a file name don t precede it with a path Prism will use the path defined in the SetPath statement if there is one If you want to import starting at a particular row or column specify them Row O is the title row and row 1 is the first row with data Column 0 is the X column and column 1 is the first Y column If you have an XY table then column 1 contains the row titles The advantage of the ImportLink command is that it lets you specify which parts of the file to import and how to rearrange the data Before creating the script Manually import a data file and choose the option to maintain a link between Prism and the data text file At this time choose options on the Filter and Placement tabs of the Import dialog to select rows and columns to import and rearrangements such as transpose These properties are stored with a data object See Data objects in Prism The ImportLink command then replaces new data using the same properties If there is only one data object on the table don t specify row column or subcolumn Prism simply uses the only data object on the table If there is more than one data object you
90. tab to place additional ticks or lines formerly called Custom Ticks on your graph You can create as many grid lines anywhere on an axis Using a grid to align objects Right click anywhere on the Prism toolbar and choose Show Grids or drop the View menu and choose Show Grids This grids will not show in printouts or exported images Hide Main Toolbar Hide Bottom Toolbar Show Rulers Inches Centimeters 1995 2014 GraphPad Software Inc Graphs Frame and axes 277 15 1 4 Setting the graph origin The position where the X and Y axes intersect is called the origin To change the position of a graph s origin double click on the origin of a graph to open the Frame and Origin tab of the Format Axes dialog Or click on the Format Axis tool in the Prism toolbar Change P i aa KON K Eb e amp 1995 2014 GraphPad Software Inc GraphPad Prism User Guide Format Axes Frame and Origin X axis Left Y axis Right Y ais Titles amp Fonts i Automaticall Y interse Lowes lelt Upper left X intense Lowes tight zsa Upper right lt Size Custom Size Distance of Y axis from left edge 275 in Width Length of X ans 30 in Distance of X axis from bottom edge 4 43 in Height Length of Y axis 200 in Axes and Colors Thickness of axes lp X Color of plotting area Clear r Color of axes m Page background Clear X Frame and Grid Line Frame style No frame X Hi
91. test data gt i A Heig DB LOL ATE Mea T GaQu as l HEH X rew 9 D Saniye KEA O THe AaiBIU Pah Family W Serch results f s id Data Tables Change Graph Type amp J Unpaired t test data Info a Graph family Column Project infol _ dh Results B Unpaired t test of Unpair es oth be bet Lob Le Jb Floating Notes I A Data with notes oes Analysis Scatter plot Piot Mean Preview Unpaired t test data 4 2 Essential concepts To use Prism effectively you need to understand these essential concepts Prism data tables are organized It is essential to choose the right kind of data table Unlike Excel or most statistics programs Prism s data tables are organized with a structure or format To use Prism effectively therefore you must learn the distinction between the six types of data tables Don t try to choose the kind of table based on the kind of graph to make That approach doesn t always work Choose a table based on the organization of your data and the analyses you wish to perform APrism project can contain many data tables and graphs A Prism project another term for a Prism file is not limited to a single graph or 1995 2014 GraphPad Software Inc 52 GraphPad Prism User Guide data table but rather can contain up to 500 data tables graphs analyses and page layouts Prism can automatically plot error bars from raw data On
92. text for each row title This is new to Prism 6 You may also now bold italicize and underline text in titles you could always use superscript subscripts and Greek To add an additional line of text to the title click the Line Break symbol or press the key combination Shift Enter to move to the next line Table format Grouped Autocomplete Prism uses autocomplete to help you It tries to guess what you are typing and let s you choose from a list of titles you ve used before If you find this more annoying than helpful turn it off in the View tab of the Preferences dialog Showing row titles on a graph 1995 2014 GraphPad Software Inc Data tables 135 Double click on any symbol to open the Format Graph dialog and choose Label each point with its row title Double click on any row label to change the font of all the labels You can also delete individual labels or drag them to a new location Additional options Plot ox Left Y axis Show legend Right Y axis A Dog diet results 50 45 Bowser 40 6 3 Fido 2 30 25 EM Rex 20 Poochy 15 10 5 0 Week 1 Week 3 Infant Mortality vs GDP 2 e Sierra Leone SREB IMR eo8S 88885 0 5 000 10 000 15 000 20 000 Real GDP per capita 10 8 Sorting data Reordering XY data If you choose connecting lines on an XY graph Prism connects the points in the order they appear on the data table If the data are not sorted on the data
93. than 1 0 with no upper limit On a log scale in contrast ratios are symmetrical A ratio of 1 0 no change is halfway between a ratio of 0 5 half the risk and a ratio of 2 0 twice the risk Thus plotting ratios on a log scale as shown below makes them easier to interpret The graph below plots odds ratios from three caseLicontrol retrospective studies but any ratio can benefit from being plotted on a log axis p Snow 1999 Snow 1999 Raine 2003 Raine 2003 Sohn 2002 Sohn 2002 Jew www wee wwe eee 0 1 10 0005 1 0 15 202530354045 Odds ratio Odds ratio The graph above was created with the outcome the odds ratio plotted horizontally Since these values are something that was determined not something set by the experimenter the horizontal axis is the Y axis even 1995 2014 GraphPad Software Inc 310 GraphPad Prism User Guide though it is horizontal A logarithmic axis linearizes compound interest and exponential growth The graphs below plot exponential growth which is equivalent to compound interest At time 0 0 the Y value equals 100 For each increment of 1 0 on the X axis the value plotted on the Y axis equals 1 1 times the prior value This is the pattern of cell growth with plenty of space and nutrients and is also the pattern by which an investment or debt grows over time with a constant interest rate 150000 100000 100000 10000 50000 1000 0 100 ee ee 0 20 40 60 80 0
94. the script that Prism will launch Include the symbol in front of the script name Two important notes e Prism will run invisibly Even when it is done Prism will not show on screen e As soon as Visual Basic has launched Prism it will continue to the next statement in the Visual Basic program or macro It will NOT wait for Prism to complete before continuing If you don t take the extra steps described below your Visual Basic program will try to read a file containing Prism s results before Prism has finished creating that file To avoid this make your Visual Basic program pause until Prism creates a file as explained below When you write the Prism script include lines at the end of the script to create a file that will tell Visual Basic you are done The example below creates done txt OpenOutput done txt WText done CloseOutput 1995 2014 GraphPad Software Inc a GraphPad Prism User Guide Your Visual Basic code should first delete the file done txt if it exists from a previous run and then launch Prism Immediately following include these lines that make your program loop until done txt is created Do Until Dir C prism 6 done txt gt Application Wait Now TimeValue 00 00 1 Loop The first line in the example above checks whether the file done txt exists Change the path and file name as needed If the file exists Prism is done Visual Basic continues beyond the loop with any code th
95. the exported file 21 2 Exporting options File format This is the most important choice If you don t want to think about it we suggest using PDF if you can and use TIFF as a second choice 1995 2014 GraphPad Software Inc Exporting images from Prism 385 Read about the pros and cons of the alternative formats Clear transparent background Within Prism there is no distinction between having a clear page background and a white background When you paste or export a Prism graph into another program however the two are distinct if the exported graph is combined with other objects that are behind in a front to back sense it If the background is clear you ll see other objects that are behind it If the background is white you won t The PDF EPS WMF Windows only and EMF Windows only formats allow you to choose a transparent clear background If you choose to export as a TIF file you can choose a transparent background if you use Prism Mac but not with Windows The JPG PNG PICT mac only and BMP formats simply have no concept of a clear background so those file formats simply don t allow for the possibility of clear backgrounds Resolution The resolution is entered in dots per inch dpi For perspective most computer screens have a resolution of about 100 dpi and most professional printing presses used by journals use a resolution of 1200 dpi Laser printers range from 300 to 1200 dpi The PD
96. the number of pages needed to print a table To do so click the Zoom buttons Or use the keyboard shortcuts Use Smaller Font Ctrl J Use Larger Font Ctrl M QQ Note these buttons work differently in data and results tables than they do in graphs and layouts When you are working with a table the zoom buttons 1995 2014 GraphPad Software Inc Printing s change the actual size of the font used which will then change the size of the printed table When working with a graph or layout these buttons simply zoom what you see on screen but do not change the actual size of the graph or layout when printed Portrait vs landscape Save paper with some tables by changing the Landscape Portrait orientation when printing data tables results and info sheets Go to File Printer Setup for Windows File Page Setup for Mac A single setting applies to all data tables results sheets and info pages in the entire project Note that the Flip button which changes graphs and layouts from portrait to landscape orientation doesn t work on data or results tables Change column widths Reduce column widths by positioning the cursor between column headings and dragging to squeeze more onto each printed page Printing preferences Three options shown on the File amp Printer tab of the Preferences dialog affect printing of tables Print grid lines on tables Check this box to include the horizontal and vertical lines on d
97. the Clear option if you want point to point lines and overlapping points to show through the open symbol Use the Shape drop down menu to select one of Prism s symbols Use the More option on this drop down to use any character from any font on your computer as a symbol Shape v s G08900090 lises EOM k Da E 25 w N AYAVAAVY w w Cats OOF R i LOR 15 7 tx Dogs 0400908 XFO Fg Ata nA Ad Ain eee 0 5 10 15 20 25 ee wee ee N o Show bars spikes drop lines Use this setting if you want to drop vertical bars from your data points The bar will start at the X axis or whatever Y value you choose and go up or down to the Y position of the point This is useful when you want to create a bar graph where each bar s position is determined by its X value It is also useful when you want to combine points and bars on one graph as shown below If you pick the narrowest width for the bars the bars will actually be spikes suitable for graphing mass spectra V Show bars spikes droplines Coke ME Wek 7 WO Border col ME 3 Bars begn aY 0 00 Pattes a v Bordes thickness 1 pt v i 30 6 25 5 20 4 15 3 10 2 5 1 0 0 1 2 3 4 5 6 0 25 50 75 100 Bin Center Show error bars Choose the format and color of error bars Choose dotted or solid lines to show an error envelope as in the graph on the right below Use the Show Area Fill button to add fill between the limits of the error envelope Learn more
98. the dialog light blue in the example and drop onto one of the custom color boxes To choose a custom color click on it Troubleshooting the Mac color picker Selecting colors Windows Within Prism there are color drop downs on many dialogs Format Graph Format Axis and on some right click shortcut menus Choose a color shown and you are done Or click the bottom choice More Colors for more choices This brings up the custom color dialog which is part of Windows and was not created by GraphPad Choose Color nn a 2 D O 2 fa s BEER a 2 3 o 2 a 2 E En Sees EHE EENEN EE EEEE EHE EEEE Use these custom colors in new projects Hue 160 Sat 240 a Lum 120 Color Solid Red 0 Green D 7 Blue 255 Add to Custom Colors 1995 2014 GraphPad Software Inc Prism Graphs the basics 203 There is room at the bottom left of the dialog for 16 custom colors you create To define and save a custom color follow these steps 1 Make sure that Use these custom colors in new projects is checked 2 Check on one of the 16 custom color boxes in the bottom left of the dialog an empty one if there is one empty 3 Choose a color by clicking on the large box of colors at the upper right or by entering RGB or HSL values See the note below about the intensity slider 4 Click the button Add to Custom Colors The color will appear in one of the 16 cust
99. the objects one at a time Or drag an imaginary rectangle around all the objects You ve selected all objects entirely contained within the rectangle Moving objects To move an object with the mouse Point to an edge Press the left mouse button and drag To move an object vertically or horizontally only With Prism Windows Hold the Shift key while dragging to allow only vertical movement Remember this because the Shift key is marked with a vertical arrow Hold the Ctrl key while dragging to allow only horizontal movement With Prism Mac Hold the Shift key Prism will let you drag vertically or horizontally but not at an angle To prevent automatic snapping Hold the ALT key down while dragging an object to prevent Prism from trying to automatically snap it into place To nudge an object a tiny distance Select one or more objects Press the up down right or left arrow keys Each press of an arrow key moves the object s one pixel To nudge an object in larger steps Hold down the Control key Windows or Command key Mac and each click of an arrow key will move the objects in larger steps To group two or more objects so they move together Select Group from the Arrange menu or toolbar 1995 2014 GraphPad Software Inc Adding text drawings and pictures to graphs or layouts 379 EDO TA Align Objects gt Center on Page Send to Front Send to Back Ctr G Lock Object Duplicate Object Ctr
100. the one that was selected when the file was saved Any 1995 2014 GraphPad Software Inc GraphPad Prism User Guide other worksheets are invisible to Prism When importing data from an Excel file Prism launches Excel invisibly and asks Excel to send the data to Prism So Prism can only import an Excel file if Excel is available on the same computer as Prism Because Excel has to be launched in the background importing an Excel file can take much longer than importing a text file Importing an Excel file requires an OLE Object Linking and Embedding connection between Prism and Excel This is a complicated process requiring the coordination of Excel Prism and various Windows components While it works fine on most computers it simply doesn t work on some computers Because Macintosh computers don t support OLE importing Excel files directly isn t possible with Prism Mac You ll rarely want to import an entire Excel spreadsheet into Prism While you can restrict rows and columns to import on Prism s Import dialog in most cases it is easier to simply copy and paste the appropriate range Importing text files All spreadsheet and statistics programs can export blocks of data as a text file separating adjacent columns with commas semicolons or tabs Text files commonly have extensions such as TXT DAT CSV comma separated value or PRN printer Some programs refer to these files as ASCII files rather than text files
101. time over clicking OK to see the changes then bringing back the dialog to make more changes l Change Graph Type l Help Cancel Apply D 1995 2014 GraphPad Software Inc Prism Graphs the basics 195 13 4 Changing the type of graph Click to open the Change Graph Type dialog Choose one of the thumbnails showing the various kinds of graphs and inspect the preview below to make sure it is the graph you want This dialog is really designed to let you change graph type within a family For example change from column chart with error bars to a scatter plot It also lets you change to a graph in a different family but this rarely makes sense If you need to change to a different family of graphs there is a good chance you also need to change the format of the data table You can also change graph type within the Format Graph dialog Click Global upper right corner of dialog then change all data sets so the changes you make apply to all the data sets and not just one 13 5 Changing which data are plotted Key points about plotting data sets Once you understand these key points it will be easy to control which data sets are graphed e A graph can include many data sets from many tables By default Prism makes one graph per table But you can plot the same data table on multiple graphs and a single graph can have data from multiple tables e When you fit a curve by nonlinear regression o
102. to format the table for entry of preaveraged data Enter and plot error values already calculated elsewhere Enter Mean SD N x Here is the list of choices Mean SEM N Mean ZC N Mean amp SD Mean amp SEM Mean amp ZEY Mean Error Mean Upper Lower Limit If you enter mean and SD or SEM why also enter n 1995 2014 GraphPad Software Inc Error bars and replicates 155 If you only want to make a graph showing mean and SD or SEM you only need to enter those values into the data table It is ok to omit the n values or to format the table for entry of Mean with SD or SEM but without n It is necessary to enter n in these situations e You want to be able to switch between graphing SD SEM and CI error bars If you enter SD or SEM with n Prism can switch between plotting whatever form of error value you want to show e You want to do statistical analysis t tests ANOVA and more require knowing sample size e You want accurate nonlinear regression If you enter the data as mean and SD or SEM Prism will fit the means and ignore the values you enter as SD or SEM If you also enter n Prism can account for scatter and sample size and the curve fit will be the same as if you had entered raw data What is the CV The CV is the coefficient of variation as a percentage so is defined as 100 SD Mean Since the SD and Mean are in the same units the CV is a unitless percentage The d
103. values as Y It computes a predicted Y value from the line at each value of X Finally it subtracts or divides this predicted baseline Y value This method is appropriate when you know that the nonspecific or background values must be linear with the X values for example nonspecific binding is often linear with ligand concentration and is particularly useful when you have not collected baseline or nonspecific measurements at every value of X Prism will fill in the missing nonspecific values from linear regression When Prism 1995 2014 GraphPad Software Inc Transforming normalizing etc 353 fits linear regression it does not assume that the line goes through the origin and does not display the regression results e The mean of all the values in say column A You need to approach the calculation differently if you wish to define the mean or median of one column to be the baseline to subtract from or divide into all the other values You cannot accomplish this goal using Prism s Remove Baseline analysis Instead do two analyses of your data table First do a Column Statistics analysis to compute the column means Then do a Transform analysis and choose the transform Y Y K or Y Y K Hook the value of K to the mean of the column you wish to use as the baseline usually the first column as computed by the column statistics analysis Calculation The choices are self explanatory You can ask Prism to subtract the
104. way to take Prism data or results and place into Word or PowerPoint is via copy and paste If you do this you ll find that Prism s tables remain tables when they are pasted In contrast if you export then import a text file Word or PowerPoint won t format it as a table When pasting into Excel or some other spreadsheet or statistical program note the options at the bottom of the File amp Printer tab of the Preferences dialog Choose whether you want excluded values copied and whether you want the decimal separator to be a period or comma Exporting Prism data From any data or results table click on the Export button on the toolbar and choose the format you want to use Export TXT XML 1995 2014 GraphPad Software Inc Importing and exporting data 187 Epos ose cm ata Where to export File Data 1 Browse Enter fla name oriy without file ype exterisior Folder C Users Harvey Documerts Select Open this folder aftes exporting Exporting options Format TAT Tab delimited text i i Decimal separator Pataj Column ites Include X Delaults Make these opbone become the delaulls except for folder which is set in preferences Restore the orignal delau amp ts Exporting format You also can specify how to handle excluded values how to format the decimal separator and whether or not to include column titles CSV CSV stands for comma delimited values but the name is a bit misleading In the
105. what you downloaded or purchased 1995 2014 GraphPad Software Inc Support and license s a The free demo version may be used for a period of 30 days from the date that you first install it Once this 30 day period has expired you must either purchase a permanent license to use the Software or promptly destroy all copies of the Software in your possession Any attempt to defeat the time control disabling function in the Software is a material breach of this Agreement and a violation of intellectual property law b A perpetual license does not expire and may only be terminated by GraphPad if you violate the terms of this Agreement Upgrades to newer versions are not included Each perpetual license may be installed on one computer If that computer is used exclusively by one person and not shared with others then that person may also install the Software on a second computer also used exclusively by him or her c A personal subscription lasts for the period of time for which you subscribed as indicated on your invoice for the Software and may only be earlier terminated by GraphPad if you violate the terms of this Agreement A personal subscription may be installed and activated twice on computers used solely by the subscriber Upgrades to newer versions during the term of the license are included You acknowledge that i your right to install and use the Software is limited to the term of your subscription ii the Software
106. you later import an XML file everything should just work There is no ambiguity about whether commas are for decimals thousands or used to separate columns If your goal is to export a data table from Prism on one computer and import it into Prism on another computer you should choose XML format While Prism follows standard XML conventions the way Prism denotes unique features such as subcolumn excluded values floating notes etc is unique so files can t be directly imported into other programs without some extra work An XML style sheet is appended to every XML file exported That means you can view the file in a web browser and see your data tables as tables But don t be fooled by this You are not viewing the XML file you are viewing a rendition of the file as specified in a style sheet that is appended to every XML file Prism exports To see what the file actually looks like use a text editor We provide the XML schema in the Prism program folder prism6xmlischema xml Using that and by exporting sample files from Prism a programmer could enable other programs to export data in Prism XML format In addition to exporting data tables as XML Prism can save an entire project in a new XML based file format PZFX More choices when exporting or copying data How should excluded values be handled The idea of excluding values is unique to Prism so there is no standard way to denote exclusion when exporting data Prism 6 off
107. you put a at the mean The location of the whiskers Prism offers six ways to create whiskers in box and whiskers plots e Min to max The whiskers go down to the smallest value and up to the largest e Tukey See details below e 10 to 90 percentiles The whiskers are drawn down to the 10th percentile and up to the 90th Points below and above the whiskers are drawn as 1995 2014 GraphPad Software Inc 23 GraphPad Prism User Guide individual dots e 5 and 95 percentiles e 2 5 and 97 5 percentiles e 1 and 99 percentiles e Min to max show all points This method plots whiskers down to the minimum and up to the maximum value but also plots each individual value as a dot superimposed on the graph Details of the Tukey method for plotting the whiskers and outliers 1 Calculate the interquartile distance the difference between the 25th and 75th percentiles Call this the IQR 2 Add the 75th percentile plus 1 5 times IQR If this value is greater than or equal to the largest value in the data set draw the upper whisker to the largest value Otherwise stop the upper whisker at the the largest value less than the sum of the 75th percentile plus 1 5IQR and plot any values that are greater than this as individual points 3 Calculate the 25th percentile minus 1 5IQR If this value is less than the smallest value in the data set draw the lower whisker to the smallest value Otherwise stop the lower whisker at the lowes
108. zoom buttons Zooming changes the magnification on the screen but does not change the size of the graph or layout when printed Hold Ctrl and press M to zoom larger or J to zoom smaller Rulers Se ee S 1995 2014 GraphPad Software Inc 382 GraphPad Prism User Guide Choose Rulers from the View menu The rulers appear on top and to the left of the graph and page layout screens Show the rulers to align objects precisely Hide the rulers to leave more space for the graph Alignment guides ey IS Maana ee d ee Alignment guides are temporary lines you can drop from the ruler to check on the position and alignment of objects Click the mouse in either ruler to drop a single guide down from the top ruler or over from the left ruler Click the corner where the two rulers intersect to drop both alignment guides at once The guides will remain visible only as long as you hold down the mouse button Grids Ve Me Pet Renton tote en ee ee ee ee Choose Grids from the View menu Prism will show a grid that extends from the minor ticks on the rulers spaced every 0 1 inches or 1 millimeter This grid is provided to help you align objects It will not print Select Grids from the View menu again to turn it off Note the distinction between showing this grid and choosing a frame with a grid from the Format Axes dialog to include a grid on a graph 21 Exporting images from Prism 1995 2014 GraphPad Software
109. 0 Value Baseline Baselne Subcolumns Repeated measures When computing results for the Y2 subcolumn only consider baseline values inthe Y2 subcolumn Repicates No matching Average the baseline replicates and do calculations with the average Ignore subcolumns Average al replicates and only do calculations with the mean values New graph Create a new graph of the results Definition of baseline Depending on the experimental details the baseline can be defined in at least three ways Think this through before choosing this analysis in Prism The baseline value for a particular value can be e A value or the mean of several replicate values in specified rows of the same column as the total value Choose to define the baseline as the value in the first row the last row or the mean of a specified number of values in the first and or last rows e A value or mean of replicate values in the baseline column of the same row of the table as the value from which the baseline will be subtracted or divided So the baseline value for a value in row 13 of column B would be the value in row 13 of column A or the mean of replicate values in row 13 of column A Choose between a single column being the baseline values for all other values or of having every other column be baseline vs total If you check the option to assume a linear baseline Prism performs linear regression using the X values as X and the background nonspecific
110. 0 45 gets rounded down to 0 4 These are both correct since rounding a 5 up or down is an arbitrary decision Prism Windows uses the C function sprintf to display real numbers A Microsoft knowledgebase article explains how this function rounds The function used by the Mac Xcode compiler is similar but not identical Note that Microsoft Excel is different It uses two methods one when the calculation is done within a worksheet and another when done by a macro It doesn t really matter in most cases What you see on the Prism data table matters only when you look at that table Notes e Choosing to show fewer digits on the data table won t affect how Prism analyzes or graphs your data Analyses are always based on all the digits you entered up to the seven Prism can store e When you save the Prism file as PZF or PZFX Prism saves all the digits you entered up to seven so the values are not truncated when you save e When you copy data from a Prism data table to the clipboard Prism copies the values you entered not only the digits you see on the table e When you export a data table as a TXT or CSV file Prism exports the digits you entered and not only those that appear on the table 1995 2014 GraphPad Software Inc Error bars and replicates 147 11 Error bars and replicates Prism lets you enter error values directly in a data table and plot them on a graph or it will calculate them from raw data You can ch
111. 00 5 00 interchanging X and Y When you choose a standard function you can choose to interchange X and Y values and also choose transforms of X or Y or both Some notes on interchanging X and Y values e Prism can interchange data on tables with more than one data set more than one Y column even though the results sheet has only a single X column It does this by creating additional rows The results will be staggered down the page with only one data set in any particular row If you entered replicate Y values or mean with SD or SEM Prism interchanges X and Y by putting the mean Y value into the X column Information about the scatter of Y is ignored If you selected X or Y transforms in addition to interchanging Prism applies the transform to the data after interchanging X and Y This means that the X transform is applied to data that were originally in the Y column and the Y transform is applied to data originally in the X column Transforming error values If you entered replicate Y values Prism can transform each replicate or the mean of the replicates If you entered data as mean SD or SEM and N Prism tries to transform the error bar as well as the mean When a transform is intrinsically asymmetrical i e logarithms it is mathematically impossible to transform a SD and end up with a SD You have two choices You may either transform the mean only or erase the error bars Or you may convert the error bars to 95
112. 1200 dpi but some journals prefer 300 dpi Definitely avoid the 100 dpi resolution which is way too low for publication Some of our customers say they always give the journal more resolution than requested and this seems to work well for them e Choose the color model requested by your journal Different journal have different requirements It seems that RGB is now more popular than CMYK so choose RGB if you don t know what your journal wants If your graph is entirely black on white choose the monochrome or gray scale color model e For size choose to make the exported file the exact width the journal wants More e For compression choose the LZW method as it is standard and should not pose any problems to the journal production process Exporting as an EPS file EPS files encapsulated postscript files encode the graphs as vectors and fonts so have infinite resolution except for any embedded pictures They are more compact and sharper than TIFF or other bitmap files Even if the journal you are submitting to doesn t list EPS as an acceptable format ask them since their printed guidelines may be out of date 1995 2014 GraphPad Software Inc 390 GraphPad Prism User Guide The problem of fonts in EPS files Prism Windows but not Mac offers an option to convert fonts to outlines when exporting to an EPS file The default is to save the text as characters with references to the font If you have used only standard
113. 14 GraphPad Software Inc 322 GraphPad Prism User Guide 16 4 Repeating an analysis If you have already entered data on a new data table and want to analyze it exactly like you have already analyzed an existing table use the Wand Wizard to ANalyze Data If you haven t yet entered the new data consider duplicating the current data table with its family Then edit or replace the data on the new table and the analyses will update If you have placed parts of the analysis on the graph regression lines or curves or copy and paste a results table then you can clone that graph 16 5 Frozen and orphaned analysis results Prism hot links data to analysis results If you change the data Prism will automatically recalculate the analyses and update the results It will also update any result tables that have been embedded onto graphs or any result values that have been hooked to dialogs If you delete a data table any linked results become orphaned and you ll see the word orphaned in the bar at the bottom of the Prism window When the data table is gone you can view and graph the orphaned results but you cannot change the parameters Note the distinction between deleting a data table and deleting all the values If you erase all values from a data set using the DEL key Prism still maintains the links between the data and the results Since there are no data the results 1995 2014 GraphPad Software Inc Analyzing data with
114. 1995 2014 GraphPad Software Inc Exporting images from Prism 39 choice we let you choose whether Prism copies EMF WMF or both Choose at the bottom of the File amp Printer tab of the preferences dialog If you re having problems with pasted graphs looking funny try setting another format as the default choice for copying and pasting Preferences O eats Co Into ss Locations Send to MS Office View J New Graphs Analysis Intemet Automatic backup J Ever time a diferent sheet is viewed YiEvey 5 minutes File Format PZF 6 PZFX Cannot be opened by Prem 4 but data and nfo ae in XML foemat that other programs can access Do not save for read page size to cr from pef file Save compact smaller but requres recalculahons after opening J Always prompt when saving to a temporary folder Print Options s Print grid lines on tables Piint no gays and no colors Print row and column labets Print sheet name as header Copy to clipboard Oe lt lt Copy graphs and layag ti EMP ON an F Background color a Copy excluded valua Decimal separator 21 10 Embedding or linking Prism graphs in other programs This page applies only to Prism Windows There is no Object Linking and Embedding on the Mac The difference between pasting an object a link or a picture There are three ways to copy a Prism graph or layout and paste it into many Windows programs including Word or PowerPoint Past
115. 20 40 60 80 Time Time The graph on the right is identical to the one on the left except that the Y axis has a logarithmic scale On this scale exponential growth appears as a straight line Exponential growth has a constant doubling time For this example the Y value cell count value of investment doubles for every time increment of 7 2657 Exponential decay is also linearized on a logarithmic axis but only when the decay eventually decays to zero 15 3 6 Advice Bar graphs with log axes rarely make sense Prism can create bar graphs with a logarithmic Y axis but think twice before deciding to make this kind of graph The point of a bar graph is to let people compare heights or areas of the bars In most cases you should try to avoid using a log axis when creating a bar graph The treated bar in the graph below with a linear axis is four times as tall and has four times the area as the control bar This tells you that the treatment 1995 2014 GraphPad Software Inc Graphs Frame and axes 311 increased the response fourfold This is very straightforward since the Y axis is linear 1000 400 Control Treated Beware of bar graphs with a logarithmic axis Since zero can t be shown ona log axis you need to decide where to begin the axis A log scale has no logical starting place so the choice is arbitrary The graphs below show the same data as the graph above but with the Y axis beginning at 0 001 10 or 100
116. 4 GraphPad Software Inc so GraphPad Prism User Guide GraphPad Prism Projectl Unpaired t test of Unpaired t test data ta File Edt View Insert Change Arrange Window Help Fue Sheet Undo Clipboarc Araian Intersret D B HAr o XG Pe Xn 9e OD E aae f r Faenily P Search results ta ties gt Ib Dete Tebles ip Unpaired t test data SH info Project infol gt Ib Results E Unpaired t test of Unpa p Graphs IE Unpaired t test data fh Layouts g Floating Notes a 3 Date with notes 4 Table Analyzed Unpaired t test data vs Columa 8 a T Unpaired t test 0 Are means signif different P lt 0 05 sr es KT 1 2 3 Column A 4 5 oa 13 14 How big is the diference 2025 ONS 5 00 6 708 Na FAT Diterence between means 10 802 9010 18 95 confidence interval 31 18 to 9 583 19 R square 1377 F test to compare vanances F DFn Dfa 680 5 4 P value 6354 P value summary Are vanances significantly different S N E 3 3 D 5 In the navigator on the left click on Unpaired t test data in the graphs section The Change Graph Type dialog will pop up Choose the kind of graph you want and see how that choice will look We suggest choosing a Scatter plot and plotting a line at the mean 1995 2014 GraphPad Software Inc Getting started with GraphPad Prism 51 GraphPad Prism Projectl Unpaired t
117. 76 79 81 87 99 ea Grouped tables The idea of two way variables is best understood by example One grouping variable male vs female in the example below is defined by rows the other grouping variable control vs treated is defined by columns 87 5 321 5 109 4 111 2 ae me a Bes A anne tN BIR BA oP ah Pah wn Arte AS onl te acum ly dete BIN te Alin he Contingency tables Contingency tables are used to tabulate the actual number of subjects or observations that fall into the categories defined by the rows and columns of a table 1995 2014 GraphPad Software Inc 112 GraphPad Prism User Guide Graf Patent Graft Obstructed Standard treatment Experimental treatment Survival tables Survival tables are used to enter information for each subject Prism then computes percent survival at each time and plots a Kaplan Meier survival plot and also compares survival with the log rank and Gehan Wilcoxon tests A 8 Parts of whole tables A Parts of whole table is used when it makes sense to ask What fraction of the total is each value This table is often used to make a pie chart The example below shows the number of students who received grades of A B C etc The sum of the five values in the table 61 is the total number of students Table format A Parts of whole Number of Students x a 1995 2014 GraphPad Software Inc Distinguishing the six kinds of data tables 113 9 3 XY
118. 95 2014 GraphPad Software Inc How Prism is unique s Constant Value Expenment Date 4 27 2012 Notebook and page 2012 33 Protocol Agonist stimulation Lot Number 545 34 Reviewed by TBO Use Info tables to record dates lot numbers concentrations etc These values can be used as constants when transforming or analyzing data Highlight sheets you want to return to i Data Tables E Exponential decay Ee Data 2 Info F Results 5 Graphs 5 Exponential decay ih t Transform of xponeni Highlight the pages that you want to review or want a colleague to look at Save to the cloud with LabArchives A LabArchives com enables researchers to store organize and publish their research data Upload your Prism files directly to LabArchives and open them even from a different computer directly from Prism s Welcome dialog Anyone can view a Prism file using the free viewer You can send Prism files even to colleagues who don t own Prism The free Prism viewer lets anyone view all parts of your files even analysis choices 3 5 Differences between Windows and Mac versions We work hard to keep the Windows and Mac versions of Prism very similar You can switch back and forth between platforms easily and files created on one platform can be opened on the other But there are a few differences Features in Windows but not Mac 1995 2014 GraphPad Software Inc a GraphPad Pris
119. 995 2014 GraphPad Software Inc Adding text drawings and pictures to graphs or layouts 381 E Select Align Objects from the Arrange menu or toolbar Choose horizontal and vertical orientation or to align by the X or Y axes To position an object by entering distances Select Position Object from the Arrange menu or toolbar Enter the distance of the upper left corner from the top and left edge of the page To lock an object so you can t accidentally move it a Select Lock Object from the Arrange menu or toolbar When you select a locked object the knobs will be gray rather than black and you will not be able to move the object or change its size To unlock the object select it then select Lock Object from the Arrange menu again To bring an object on top of overlapping objects i Select it drop the Arrange menu or toolbar and choose Bring to Front To send an object behind overlapping objects Select the object Drop the Arrange menu or toolbar and choose Send to Back To space objects equally a Select three or more objects Choose Distribute Objects from the Arrange menu or toolbar To duplicate one or more objects Select the object s Drop the Arrange menu or toolbar and choose Duplicate Object To center everything on a page a Click the Center button Zoom settings QQ To precisely align objects zoom to a larger magnification Select a zoom level in the View menu or click the
120. A ei fog Thousands Power of 10 Anjio When you choose to label the X axis with row titles the spacing of the points may change Essentially Prism uses the row number as the X value so the points will be equally spaced along the X axis even if the X values are not evenly spaced By default each row label will appear If you have many rows this will be cluttered You can ask Prism to plot say every fifth row label by changing the major tick interval to 5 starting at 0 Keep in mind that Prism uses the row number first row is 1 rather than the values entered into the X column to position the data and determine which labels to show Prism also uses this coordinate system row numbers when positioning additional ticks and grid lines If you ask for a grid line at X 5 Prism will draw it to correspond with the point in the fifth row whatever its X value 1995 2014 GraphPad Software Inc 22 GraphPad Prism User Guide Grouped and contingency table graphs With Grouped graphs and graphs of contingency tables you can have a choice of labeling the X axis with row titles column titles or row number You may or may not see all three choices depending on how you configured your graph Format Axes Fiame and Ogn as Lett ands Aight Y eas Titles amp Fonts Gaps and Direction nad Scale Automaticaly determine the range and interval Range row numbers It i not possible to change the range of this axis All tic
121. AM and hard disk space We ve tested hundreds of thousands of rows e Up to 256 data set columns Prism 5 only allowed 104 e Up to 256 subcolumns Prism 5 only allowed 52 If your table has more columns or subcolumns that Prism 5 can handle the table will simply not be included when you open the file in Prism 5 10 3 Changing a data table format The choice you make about how to format your data table is important If you don t choose the appropriate kind of data table you won t be able to make the kind of graph you want or perform the analyses you have in mind 1995 2014 GraphPad Software Inc Data tables 123 For XY tables Prism uses subcolumns replicate data If your table needs more subcolumns you can always change the number of subcolumns replicates in a data table Or if you entered already calculated error values but your table is labeled wrong say you actually entered SD but the table is formatted for SEM you can make the switch To change the format of a data table Click on the Table format area in the upper left of a data table X Group A conc pM Binding fmol ma xX Y 10 1 25 2 26 4 36 5 35 6 40 7 40 8 42 9 43 10 44 115 45 12 45 at Alternatively click on the Table Format button on the Change toolbar 1995 2014 GraphPad Software Inc 1 GraphPad Prism User Guide Format Data Table oe fae Table Format Column Titles Data table Kind of table XY J Show row t
122. Click on the button on the Prism sheet You must have your speakers turned on to listen to audio notes To delete an audio note Select an audio note and hit the Delete key 6 6 Highlighting sheets in the Navigator tree Highlight a sheet name to remind yourself to go back to it or to flag sheets you want a co worker to view Select a sheet in the Navigator or several sheets in the Gallery and click on the Highlight button on the Sheet toolbar 1995 2014 GraphPad Software Inc Organizing Prism projects 89 Family a Search results H Data with Results Fransform of Data 1 Ti Nonlin fit of Transform of Data 1 l Table of results 1A Curve i Normalize of Transform of Data 1 3 Nonlin fit of Normalize of Transform of Data 1 L Table of results I Curve Data Tables Info 5 Results 3 B Graphs tanstorm of Data 1 graph l Normalize of Transform of Data 1 graph B Layouts fg Layout 1 Pt Floating Notes 6 7 Preferences Use the Preferences dialog to set Prism s defaults for various settings Note that some preference settings are made elsewhere The import paste special dialog the export graph and the diagnostics tab of nonlinear regression for example all have check boxes to make the current settings default for the future To open the Preferences dialog drop the Edit menu Windows or Prism menu Mac and choose Preferences Preferences a ed O m InfoShee
123. Click the magic wand button on the toolbar to bring up the Analyze Data dialog Analysis Ke Sanalyze J 3 Choose the existing data table in the current project you want to use as an example 4 At the bottom of the dialog optionally enter the prefix you wish to appear in front of the new sheet names 1995 2014 GraphPad Software Inc Work efficiently Repeat analyses and graphing 97 That s it The new table where you started from will be graphed and analyzed the same as the example table Notes e The name Wand is new to Prism 6 This feature used to be called Applying a Method e You can also choose to use the Wand to apply a stored method file To save a method file go to the data table that has been analyzed and graphed drop the File menu and select Save Special Save Method Where is it saved To apply that saved method file click the Wand button or the Analyze button and then choose Use Saved Method at the top left of the Analyze Data dialog e The same icon is used for both the Magic and Wand features Magic Make Graphs Consistent changes the appearance of selected graphs so they look like an example graph You can only use Magic when you start from a graph or a set of graphs selected in the gallery The Wand analyzes and graphs a new table the way you have already analyzed and graphed another table You can only use the Wand when you start from a data table with data 7 4 Templates What is a t
124. Clone A Graph tab of the Welcome dialog Saved examples 1995 2014 GraphPad Software Inc Standardizing Prism use in a lab a Prism Windows XP saves examples in system disk Documents and Settings User Application Data GraphPad Sof On Vista or Windows 7 Prism saves examples in system disk Users User AppData Roaming GraphPad Software Prism 6 0 Ex Prism Mac saves these files in Users User Library Application Support GraphPad Prism 6 Examples exam Shared examples The Welcome dialog cloning tab offers a separate tab for shared examples These are intended to be examples created in a lab to be shared with everyone in a lab The only way to show graphs on this tab is to manually move filed from the saved example folder to the shared example folder On Windows XP Prism looks for shared examples in system_disk Documents and Settings All Users Application Data GraphPad On Windows Vista or Windows 7 Prism looks for shared examples in system _disk Users All Users GraphPad Software Prism 6 0 Examples Prism Mac looks for shared examples in Library Application Support GraphPad Prism 6 Examples Prism Mac also looks for shared examples within the application bundle Prism 6 app Contents SharedSupport Examples Providing online Help for methods and templates When you Save the template or method enter a brief description If you want to provide more extensive help to your
125. Data set First look grouped data Treated ance Lech Replicete Select Data Sets to Format Select All None Even Odd Eirst half J First look a First look J t Firstlook e Firstlook k grouped data Data SetE Firstlook grouped data Data SetF lt grouped data Data SetA grouped date Date Set B grouped data Date Set C grouped data Data Set D Click Apply to see the effect of changes The Format Graph dialog gives you a huge number of options to change the appearance of your graph Click Apply to see the effect of the changes you made without closing the dialog This saves you time over clicking OK to see the changes then bringing back the dialog to make more changes 1995 2014 GraphPad Software Inc 194 GraphPad Prism User Guide Change Graph Type Help Cancel Apply D 13 3 The Format Axis dialog Overview Double click on an axis or drop the Change menu and chose the X axis or Y axis command and the Format Graph dialog will appear Or click the Format Axis button Change Gi i KON K Eb e amp The dialog has five tabs e Frame and Origin e X axis e Left Y axis e Right Y axis e Titles and fonts Click Apply to see the effect of changes The Format Axis dialog gives you a many options to change the appearance of your graph Click Apply to see the effect of the changes you made without closing the dialog This saves you
126. EC50 Wtable Hill Slope 6 1 Write the value from the first Y column in row 6 to the next second column of the output table and label that column Hill Slope Next Loop back to the ForEach statement When the script is done table 1 will have two columns and 500 rows Each row will have the logEC50 and Hill Slope from one of the simulated experiments 23 1 4 Script example 3 Import several files onto one table This example uses the script to import several files onto one data table Script command Comments SetPath c Data Define the disk and directory to be used by the Oct2011 rest of the commands Open rapid pzt Open the Prism template rapid pzt that was created to contain a formatted data table GoTo D Go to the data section ForEach Avge_ dat Loop through all files that start with Avge_ and have the extension DAT Import Import into the first empty column Next Go to the next file which will be imported into the next column of the same table 23 1 5 Script example 4 Open a template and import data This example uses a script to launch Prism Script command Comments SetPath c data oct2011 Define the disk and 1995 2014 GraphPad Software Inc directory to be used by the rest of the commands Open rapid pzt Open the Prism template file rapid pzt GoTo D Go to the data table Import today txt Imports the file today txt GoTo G Go to the graph section While Example 4 wou
127. Eae ii aag Paste Data CtrieV 4 Paste Link Paste Data Transposed Ctrle Shift T Paste Link Transposed Paste Special Ctri Shift V aT T T T e Paste Data Prism retains no link back to the Excel spreadsheet The values will be pasted and nothing else The only advantage to using this method is that it is conceptually simpler Paste Embed You paste the selected data into the data table and also paste a copy of the entire spreadsheet file into your Prism project even if it has several worksheets tabs This means you don t need to worry about keeping track of multiple files You don t need to save the spreadsheet file separately except as a backup You can open Excel from within Prism edit the data and instantly update the analyses and graphs in Prism A potential disadvantage of embedding is that you will end up with multiple copies of the same data Another disadvantage is that your Prism files will be larger Paste Link Paste the values into the data table but also create a link back to the Excel file The link has two functions It lets you trace and document the source of the data so you stay organized It also is a live link If you edit or replace the data within Excel Prism will update the analyses and graphs The Paste Link command is available only if you paste from an Excel workbook that has a name If you are working with a new Excel file you must first save it thus giving it a name before you can link it
128. F EPS WMF Windows only and EMF Windows only formats encode vectors and fonts so have essentially infinite resolution If you export in one of these formats you will not be asked to enter a resolution The other formats offer choices of 100 300 600 and 1200 dpi If you double the dpi note that you quadruple the number of pixels in the image and thus quadruple the file size Color model If you choose the PDF EPS or TIF format you ll need to choose between RGB and CMYK color models We recommend that you choose RGB when possible as there will be fewer surprises RGB colors will closely match what you see on the Prism screen which internally uses RGB Select CMYK only when submitting images to a journal that insists on CMYK With some formats you can also choose between being able to save thousands 8 bit or millions 24 bit of distinct colors When you choose thousands of color some colors may get changed a bit when saved When you save RGB thousands of colors are stored in an indexed format but millions of colors are not Some journals may specify whether they want colors expressed in 8 or 24 bits and whether they prefer indexed or nonindexed colors 1995 2014 GraphPad Software Inc 386 GraphPad Prism User Guide 21 3 Size In most cases you ll want to export without changing the size of the graph or layout But you can specify the width of the exported graph Don t enter the desired width of the graph s
129. F 100 PZFX 100 405 QC lines 292 Questions tech support Quick print vs Print 408 Quick start 10 R Random numbers Range of axis 279 Rapid Inspector 389 RecalcAll command Reciprocal transform Recording 87 Recovering 103 Reference 461 Regenerate 422 Related sheets 71 Removing a baseline 351 Removing data from graph Renaming sheets 80 Replacing data on graph 195 Replicates plotting individual Resize layout 364 Results embedding Results freezing 322 Results orphaned 322 Reverse order of data sets 459 336 438 348 195 156 325 203 Reversing row order 135 RGB vs CMYK 391 Right Y axis 284 Rotating graphs Horizontal vs vertical 203 Rotating titles 298 Rotating transposing a data table 355 Rounding 145 Row titles 133 Row titles XY 220 Running scripts from Excel 445 Running scripts from outside of Prism 443 Running scripts using MacScript Automator or AppleScript 441 S Save command 426 1995 2014 GraphPad Software Inc Saved examples 94 Saved method 96 Saving options 100 Saving templates methods and examples files ina lab 451 Saving work 103 Scale bars axis 286 Scaling factor 364 Scatter plots which table 127 Script syntax 419 Scripts examples 413 Scripts key concept 413 Scripts launching from other programs 443 Scripts running from Excel 445 Scripts running using MacScript Automator or AppleScript 441 Scripts running within Prism 440
130. File compatibility between Prism versions Prism 6 can open all files created by earlier versions of Prism including PZM files created by Prism versions 1 to 3 Prism 5 can open all files created by earlier versions It can open both PZF and PZFX files created by Prism 6 If some Prism 6 data tables have more columns or subcolumns than Prism 5 can handle those tables will be empty in Prism 5 1995 2014 GraphPad Software Inc Prism files 103 If some analyses include options not available in Prism 5 those results sheets will show the Prism 6 results but be frozen Prism 5 does the best it can when dealing with Prism 6 choices that were not present in Prism 5 If you use two or three line row or column titles in Prism 6 these will end up on one long line in Prism 5 This works fine with Windows and with Mac if you use the PZF file format If you save the file from Prism 6 in PZFX format only the first line will be read by Prism 5 Mac and the other line s will be lost Prism 4 can open PZF but not PZFX files created by Prism 5 or Prism 6 but be careful If you open a Prism 5 or 6 PZF file in Prism 4 new Prism features will be lost so graphs may look a bit different Prism 3 and earlier cannot open files created by later versions The location of analysis results may change between versions When you open a Prism file on a version different than the version it was created on results also may appear on different rows of t
131. Fill below or above the point to point line that connects your points with a fill Specify fill color and pattern and background color You may need to adjust the front to back order of the data sets to get the effect you want 30 25 20 0 1 2 3 4 5 6 Plot on which Y axis Specify which axis to use for each data set If you choose to plot on the right Y axis Prism will create that axis if it doesn t already exist 205 10000 ia 2000 6000 104 4000 51 2000 Legend Select Show legend to create a legend for this data set Select Label each point with its row title to link the legend to the colurm title entered on the data table Uncheck this box if you don t want the legend to change when you edit the column title You can also edit the labels in the legend Double click on the legend text and type whatever you like Use the checkbox Revert Legend to Column Titles in the Legend to change the 1995 2014 GraphPad Software Inc 2te GraphPad Prism User Guide labels back to match the column titles This checkbox is only available if you have edited a legend 30 25 20 Label each point with its row title Check this box to include row titles on graph near each data point You can move each label by selecting it and dragging Even if you move a label however it remembers its position relative to the data point so when you change your data or the size and shape of your graph the labels wil
132. GREEMENT IF YOU ARE AGREEING TO THESE TERMS ON BEHALF OF A COMPANY OR OTHER LEGAL ENTITY YOU REPRESENT THAT YOU HAVE THE LEGAL AUTHORITY TO BIND SUCH ENTITY TO THESE TERMS AND ALL REFERENCES TO YOU SHALL APPLY TO SUCH ENTITY IF YOU DO NOT HAVE SUCH AUTHORITY OR IF YOU DO NOT WISH TO BE BOUND BY THE TERMS OF THIS AGREEMENT THEN DO NOT INSTALL UPLOAD ACCESS OR OTHERWISE USE THE SOFTWARE DEFINITIONS Software means the computer program identified above and in which this Agreement is embedded and any updates or error corrections thereto provided by GraphPad Computer means computers including desktop or laptop computers or file servers used for general computing functions such as but not limited to word processing e mail general purpose Internet browsing and office suite productivity tools Authorized Number of Computers means the number of Computers that the Software may be loaded as shown by the quantity of licenses purchased by you as indicated on your invoice for the Software You means you personally if you license the Software for yourself or the company or other legal entity for which you license the Software but not the affiliates subsidiaries or other related legal entities of such company or legal entity LICENSE AND TERM Subject to the terms and conditions of this Agreement GraphPad grants to you a nonexclusive nontransferable limited license to install and use the Software The term of the license depends on
133. GraphPad Prism User Guide GraphPad Software Inc www graphpad com 1995 2014 GraphPad Software Inc This is one of three companion guides to GraphPad Prism 6 All are available as web pages on graphpad com 2 GraphPad Prism User Guide Table of Contents Part I Part Il O ON Oo FPF WN N a O 13 Part Ill a fF Q N Part IV oN OO a FF WD Part V Foreword 0 How to learn Prism 10 What s new in Prism 6 12 What s new Highlights 20 cciccccesccceivie el ecetivaceecvetesectoeancceveie ss beleveecteetibeatendeecaeeiiievloeuiii ade 13 Whats new Statistics cc seccos daia aaa e aa ae aa aA eede decay cans Ara Aa iaaa EAA 14 What s new Multiple comparisonS s ssssssssusnsnrnnnnnnnnnnnnnnnnnnnnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnn nnne 17 What s new Regressi nosier caevetcevedivncs slevetes ogee voerdueveservecddvecendevetss lt geyceasusdveaestesdvent 2 19 Whatsnew PIM G SaVGIrsy ao iiciccciccccis seve e ec tsvecetiasrteedeadesseetseeeydeeadseernusscosqessduecpusdever evedvessvnce 21 What s new Data table wsiiiisicccciecsceeciecctecccsccteviis sas ecnecen cents ce tausani ainaka anaia aa 23 What s new Working with other programs ccccceeeeeseeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeneeeenees 24 What s new Parts of whole data cccceceeeeeeeeeeeeeee eee ee ee ee eeeeeeseaeeeeeeeseaeeeseeeeseaeeeeeeeenees 26 What s new Column Graphs cisiccicccccticcctesscieccccenecthicevde
134. GraphPad Software Inc 266 GraphPad Prism User Guide 14 5 Parts of whole graphs Format Graph dialog Parts of whole plots Use this dialog to change the look of a Parts of whole graph If you want to only change the look of a single segment it is simpler to use the right click menu on the graph You can also change all the symbols in selected data sets Double click on any graph section to open the Format Graph dialog Format Graph Graph type cm ie Colors amp Legends Female He Global gt Color E Sice Normal zj Show legend left to nght Color V Percentage ViVaue F Label Borders Over 1p E Internal Titles J Show graph biie E J Show totat Prefix Suffix Applicants Order AppECEN ta samisponin 2011 Standad Reverse Size Diameter 2 89 in wanes me Donut hole 50 Shape ratio Change Graph Type Hep Cancel app OK To change the general appearance of the graph Click on the thumbnail image in the Graph type section of the dialog You can change from a pie chart to a donut slice or dot plot Prism will preview how your graph will look after the change To change the settings for one data set Select a data set from the Colors and legend list and choose the color of the graph segment and what information you want the legend to show 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 267 _ To change all
135. L ecne tb et a Bring up the dialog by double clicking on the graph or using a shortcut button Cnange Pe jit pe 7 sail al wily X it ivy amp Shortcuts for adding replacing and removing data sets You don t need to use the dialog to add or remove data sets Add data to a graph by dragging a data or results table from the Navigator and dropping it onto the graph Remove or replace a data set by right clicking on any point or bar and choosing Remove Data Set or Replace Data Set Skip over some points to speed graphing 1995 2014 GraphPad Software Inc Prism Graphs the basics 197 Plotting graphs with tens or hundreds of thousands of points can be slow If you are impatient Prism lets you specify that a graph only show one out of every K points you specify K to speed up screen redrawing Choose at the bottom of the second tab of the Format Graph dialog V Graph faster Graph a row skip 9 rows graph another row f 13 6 Prism Magic Make Graphs Consistent The Prism Magic tool makes one or more graph look like another It is a huge time saver Start from a graph or several graphs selected in the Prism Gallery Click on the Prism Magic tool in the Change section of the Prism toolbar Change a n Select the graph whose appearance you d like to match You can choose from any graph in the current project or any open project any graph saved as an example or any graph recently two months pr
136. Layouts Q File Edit View Insert Change Arrange jow Help Prism File Sheet Undo Clipboard Analysis Cnange Arange Oraw Wete Text pe 08 Ze Ri Lt lA amp kk X J New i SAnalyze ES K lal ue amp a i Family J Search results H 1 Data with Results il Data Tables E Data 1 T Info Project info 1 dd Results J Transform of Data 1 L Nonlin fit of Transform o l Table of results L Curve 2 Normalize of Transform L Nonlin fit of Normalize A Table of results b ye ESetrT graph J Transform of Data 1 grap L Normalize of Transform T Layouts FA Layout 1 I Floating Notes Another way to view the Gallery is to click its button on bottom toolbar Notes e Don t confuse the Gallery which shows you all the sheets in your project 1995 2014 GraphPad Software Inc GraphPad Prism User Guide with the Portfolio which shows you a set of polished graphs you can use as examples View the Portfolio from the Welcome dialog e From the gallery double click on any thumbnail to leave the gallery and go to that sheet This is the main purpose of the gallery to help you quickly find a particular sheet and go to it e Drag and drop sheets to change their order e Click on option boxes in front of the sheet names to select multiple sheets Once you ve selected a set of sheets you can delete use Magic and much more 5 3 Graph and layout tool tips Some of the tool tips in Prism do more than provide information
137. Mann Whitney test Ordinary one way ANOVA Kruskal Wallis test These tests work fine with unequal sample size Missing values are not a problem 1995 2014 GraphPad Software Inc Data tables 141 Paired t or Wilcoxon matched pairs test repeated measures one way ANOVA Prism only analyzes rows where there are data for all conditions If one value is missing that subject row is ignored Ordinary two way not repeated measures ANOVA Enter raw data If some values are missing two way ANOVA calculations are challenging If any row column combinations have no values at all Prism cannot compute ANOVA If some row column combinations have fewer replicates than others some replicates are missing Prism uses the method detailed in SA Glantz and BK Slinker This method converts the ANOVA problem to a multiple regression problem and then displays the results as ANOVA Prism performs multiple regression three times each time presenting columns rows and interaction to the multiple regression procedure in a different order Although it calculates each sum of squares three times Prism only displays the sum of squares for the factor entered last into the multiple regression equation These are called Type III sum of squares Ordinary two way not repeated measures ANOVA Enter mean SD or SEM and N If your data are balanced same sample size for each condition entering data as mean SD or SEM and N is not a p
138. Piint no grays and no colors J Print row and column labets Print sheet name as header Copy to clipboard Copy graphs and layo EME NN a o F Background color orld mee Copy excluded valua Decimal separator Hep Cancel Editing a Prism object embedded in PowerPoint or Word To edit a Prism object embedded in PowerPoint or Word simply double click on it If you have multiple versions of Prism installed on your computer Windows will choose which version to launch the one used to create that object But you can override that decision Right click on the Prism object in PowerPoint 1995 2014 GraphPad Software Inc 404 GraphPad Prism User Guide choose the Prism Object command and then choose Convert from the submenu and choose the Prism version you want to open that object 21 11 LinkBack Mac only LinkBack lets you embed a Prism graph or layout into another program This works the same as OLE on Windows Copy the graph or layout in Prism and paste into another application Later double click on the graph in the other program and return to Prism to edit While OLE is part of Windows and supported by Microsoft LinkBack is not part of OS X and is not supported by Apple LinkBack only works with selected Mac apps It does not work with Word or PowerPoint or Keynote 1995 2014 GraphPad Software Inc 21 12 Posting graphs to a Web site To post a graph or layout to an FTP ser
139. Prism 323 become blank If you delete the entire data table the results remain and the sheet becomes orphaned If you don t want the results to automatically update when the data are changed click the freeze button in the Sheet section of the toolbar a For example you might want to freeze the results before excluding some outliers from the data then repeat the analysis and have both copies of the results in the project Click again to unfreeze When a sheet is frozen you ll see the word frozen in the status bar at the bottom of the window as well as a floating note that explains pr I tn Ey a P r 2 E aaa a e p l 31 This sheet is frozen You cannot change it and it will not update when linked data are changed 32 To unfreeze this sheet drop the Edit menu and uncheck Freeze sheet or click the Freeze button on the toolbar Tabular results 16 6 Excluding data points from an analysis Excluding individual points If a value is too high or too low to be believable you can exclude it Excluded values are shown in blue italics on the data table but are not included in analyses and are not shown on graphs From the point of view of analyses and graphs it is the same as if you had deleted the value but the number remains on the data table to document its value To exclude selected values Click the Exclude button from the Change toolbar
140. Put the insertion point at the top of Column D and choose Paste Link from the Edit menu 1995 2014 GraphPad Software Inc Importing and exporting data 163 6 Note that the pasted values in Columns A and D are surrounded by a box and cannot be edited Group A Group B Group L Group D ef Control Control Treated Treated T w 45 56 64 35 71 7 Edit a value in Column B or C Note that Column A and D are instantly updated when you move the insertion point 8 Polish the graph by double clicking on it and choosing graphing options for each data set 150 100 Activity a o Control Treated 12 3 Pasting data from Excel Windows Select a range of Excel data and copy it to the clipboard Switch to Prism move the insertion point to the cell of a data table that will become the upper left corner of the pasted data Pasting Excel data amp Then click on the Paste or Paste Special Gv button in the Prism Clipboard toolbar 1995 2014 GraphPad Software Inc 164 GraphPad Prism User Guide If you use the Paste button or the keyboard shortcut Ctrl V you will only paste the values that have been copied to the clipboard If you choose Paste Special you have several options about how you want to insert your data into Prism s data table These options are only available with Windows If you use a Mac skip to this page Clipboard Analysts Change imge la Si hie ot ge X g CG
141. Scripts to simulate nonlinear regression 342 Search for sheets 71 Second Y axis 284 Section tabs 71 Segmental axis 289 Selected sheets 81 Send to back 379 Send to front 379 Send to Word or PowerPoint 397 Sending files 106 Sending to office 89 SendToPP command 438 SendToWord command 438 Sequence of X values 143 Series inserting 143 Set Sheet Title command 420 SetAxisLimits command 424 SetAxisTitle command 424 SetGraphTitle command 424 SetInfo command 429 SetPath command 425 SetProjectName command 438 SetScriptDialogTitle command 438 SetValueTolnfo command 429 SetYReplicates command 424 Shape of graph 207 Shapes 375 Shared examples 94 Sharing Prism ina lab 448 Sheets 80 Sheets freezing 322 1995 2014 GraphPad Software Inc Index Shift enter shortcut 142 Shift space shortcut 142 Shortcuts 142 Show sheets of one type 69 Show toolbars 75 Simulating data with random error 336 Size of graph 207 skip 195 Skipping rows 356 Slide sorter view Galley 69 SmartDraw 376 Snapping text 371 Software license agreement 462 Sorting data tables 135 Sorting sheets 80 speed graphing 195 Splitting 105 Spot colors 391 Star Training 467 Starting a new data table 122 Sticky notes 87 Stretch an axis 207 Strikethough over numbers outliers 139 Subcolumn formats 122 Subcolumns on Grouped tables 150 Subcolumns on XY tables 147 Support 459 Survival data tables 118 Survival graphs 259 Syntax scri
142. To command to go to the analysis page that generates the data and use the Regenerate command to create new data with different random scatter Then go to the results write out selected results and use the Next command to loop again See script example 2 at the beginning of this chapter 23 2 5 Creating new sheets Commands DuplicateDataTable lt CLEAR gt DuplicateFamily prepend_text lt CLEAR gt Explanation For the most part script commands navigate among sheets you have already created by hand You can t create new data tables new analyses or new graphs in a script except by duplicating existing ones When you duplicate a data table all you get is a new data table You can import data into it but not analyze or graph within the script When you duplicate a family you duplicate a sheet with all linked sheets Import new data to replace the existing data and all analyses and graphs will update All new sheets include the prepended text in front of the sheet name Enter F as the prepend text to use the name of the most recently imported file 1995 2014 GraphPad Software Inc 4 GraphPad Prism User Guide 23 2 6 Changing data tables Commands SetYReplicates ClearTable lt row gt lt col gt lt subcol gt DeleteAllDataSets lt CLEAR gt Explanation Using a script you have limited ability to change a data table The SetYReplicates command changes the number of Y replicates subcolumns but script c
143. UE OR DATA BUSINESS INTERRUPTION OR COST OF COVER IN ADDITION IN NO EVENT SHALL THE LIABILITY OF GRAPHPAD FOR ANY DAMAGES ARISING OUT OF OR IN CONNECTION WITH THE SOFTWARE USER DOCUMENTATION OR THIS AGREEMENT EXCEED THE AMOUNT PAID OR PAYABLE BY YOU FOR THE SOFTWARE THE LIMITATIONS OF LIABILITY IN THIS SECTION SHALL APPLY TO THE MAXIMUM EXTENT PERMITTED BY APPLICABLE LAW TO ANY DAMAGES HOWEVER CAUSED AND REGARDLESS OF THE THEORY OF LIABILITY WHETHER DERIVED FROM CONTRACT TORT INCLUDING BUT NOT LIMITED TO NEGLIGENCE OR OTHERWISE EVEN IF GRAPHPAD HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES AND REGARDLESS OF WHETHER THE LIMITED REMEDIES AVAILABLE HEREUNDER FAIL OF THEIR ESSENTIAL PURPOSE EXPORT REGULATIONS All Software and User Documentation delivered under this Agreement are subject to United State export control laws and may be subject to export or import laws and regulations of other countries You agree not to export the Software or the User Documentation in violation of United States or other applicable export control laws U S GOVERNMENT RESTRICTED RIGHTS If the Software is being acquired by or on behalf of the United States government or a United States government prime contractor or subcontractor the Software and the User Documentation are provided with the same commercial license rights as are described elsewhere in this Agreement GOVERNING LAW This Agreement shall be governed by and construed and enforced in acc
144. Using Word to add text Windows only You can use Microsoft Word to add text to a Prism graph or layout Word gives you more formatting options than are possible with Prism text tools You can create bulleted lists add tables anything you can do with Word It s a bit more cumbersome however because you must open Word in a separate window to edit your text rather than editing it directly on your Prism sheet This is most often helpful when you have large text boxes that require a lot of formatting To add text to a graph or layout using Word click the Word button in the Write section of the Prism toolbar This willopen Word so you can create your text box To finish click on Update in Word File menu or simply close Word Write a a To edit a Word text box in Prism double click on the text in Prism This will open Word Click File Update in Word to save your changes 1995 2014 GraphPad Software Inc Adding text drawings and pictures to graphs or layouts 375 20 3 Drawing lines arrows and shapes Drawing lines arrows and other shapes on a graph 1 Click on the drawing tool in the Drawing toolbar If you want to draw several objects hold Shift while selecting the drawing tool Then you ll be able to use it repeatedly without selecting it again Click any other Toolbar button to unselect the drawing tool wange Draw Write a va Wi 1 eCO rma IF e E e he ade Note The tool you used most recently
145. WO 9 5 Grouped tables two grouping variables The idea of grouped variables is best understood by example One grouping variable might be male vs female the other grouping variable is control vs treated Every data point you collect is categorized by both grouping variables male vs female AND control vs treated A two grouping variable table and graph is used to tabulate outcomes that are measurements such as weight or blood pressure often with error bars Analyses performed with Grouped data e Two way ANOVA e Repeated measures two way ANOVA mixed model e Bonferroni multiple comparisons test e Fisher s LSD multiple comparisons test e Holm Sidak multiple comparisons test Example of a grouped table a Group A Group B Grouped Placebo Experimental A Y1 A Y2 B Y1 B Y2 45 7 56 54 3 43 3 65 6 63 3 79 0 85 74 5 71 5 112 5 124 e Unlike other programs Prism does not use separate columns to enter grouping variables Instead groups are defined by rows and columns e The rows categorize the data by one grouping variable men vs women e The columns datasets categorize the data by the other grouping variable 1995 2014 GraphPad Software Inc Distinguishing the six kinds of data tables control vs treated e Blank cells represent missing values which Prism handles properly If you are doing repeated measures ANOVA however you can t have any missing data values unless an entire subcolumn is em
146. X direction Selected data set V Nudge all points x 0 00 Y 50 00 data units Now you can see the individual tracings 1995 2014 GraphPad Software Inc GraphPad Prism User Guide T20 mv Cancer Seconds All three tracings still have about the same baseline Y coordinates But nudging the data in the Y direction separated them Because the Y values were nudged it would be misleading to plot the data on a full Y axis as in the graph above So instead the Y axis is hidden Frame and Origin tab of the Format Axes dialog and replaced with a scale bar Waterfall graphs Nudging can also help you create a waterfall graph All the data sets in the following graph cover the same range of wavelengths and all have a baseline of zero optical density Each data set was nudged in both X and Y directions each data set nudged a bit more than the previous data set This creates a pseudo 3D look that is sometimes called a waterfall Optical Density eo 33332 3 Wavelength 14 1 5 Additional XY settings The Graph Settings tab of the Format Graph dialog 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 223 Format Graph Appearance Data Sets on Graph Graph Settings For point to point connecting lines at each missing or off scale Y value Leave a gap Commect adjacent points Format of individual points To format a data point differently than the rest ext this dialog rig
147. a larger value the gaps between bars will be wider so the bars will be narrower 1995 2014 GraphPad Software Inc 230 GraphPad Prism User Guide Format Graph Appearance Data Sets on Graph Graph Settings Direction Vertical Horizontal Automatic Bars begn a Y Hide baseine sions pace between columns 50 of cokmn width Discontinuous axis Vhen the axis is discontinuous also make the bars or conmechng ines dsconbnuous Format of individual bars To format a bar differently than the rest exi this dialog tight cick on the bar and choose Format This Bar Remove all the individual formating Revert all bars to the format of their data set Change Graph Type Help Cancel Apy oko Changing the spacing between selected columns To change the space between two adjacent bars go to the Data Sets on Graph tab Select a data set and enter at the bottom of the dialog the percentage of normal spacing you want between that data set and the prior one If you enter 200 that bar will be twice as far from its left neighbor as the others If you enter 50 it will be half as far If you enter 0 this bar will touch the neighbor on the left 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 231 f Format Graph Appearance Data Sets on Graph Graph Settings Data sets plotted left to right Sample column data A Cor
148. a saved example 13 2 The Format Graph dialog Overview Double click anywhere on a graph except the axis and the Format Graph dialog will appear The choices on this dialog depend on whether you are editing 1995 2014 GraphPad Software Inc Prism Graphs the basics 193 a XY Column Grouped Contingency Survival or Parts of whole graph Change one data set several or all at once The first tab of the Format Graph dialog controls the appearance of symbols bars lines etc You can change the appearance of one several or all data sets e One data sets Choose a data set from the drop down on the top of the dialog then change the settings for that data set e All data sets Drop the Global menu at the top right of the dialog choose to change all data sets and then make the changes Any changes you make after choosing the change all data sets will apply to all the data sets Changes you made before making that choice only apply to the data set selected then e Several data sets Drop the Global menu at the top right of the dialog Choose some data sets and then change the settings for those data sets For example you could select data sets A C E and G and change all of those data sets to use a dotted line Then choose B D F and H and make those lines solid Any changes you make after choosing a set of data sets to change will apply to those data sets Format Graph Appearence Data Sets on Graph Graph Setangs
149. a simple copy and paste operation and does not use a placeholder Notes about master legends e The master legend is linked to the graph from which it was copied If you change the symbols in that graph Prism will update the master legend e Master legends on a layout have exactly the same size as the legend on the graph from which you copied the legends When you place graphs on layouts you can shrink or expand it to fill a placeholder You can t do this with master legends The only way to change the size of the symbol and lettering in the master legend is to change the font size and symbol size on the graph used to create the master legend This is done in the graphs section not the page layout section e After copying a legend you can only paste it into a layout It is not possible to paste a legend onto another graph 20 Adding text drawings and pictures to graphs or layouts 1995 2014 GraphPad Software Inc Adding text drawings and pictures to graphs or layouts 371 This section explains how to add text drawings and pictures to a graph or layout 20 1 Adding text Adding text to a Prism graph or layout 1995 2014 GraphPad Software Inc GraphPad Prism User Guide To enter new text anywhere on a graph or layout Click one of the text T tool buttons the one on the right makes a text box with a border Write va w E Click on the graph or layout at the spot where you want to enter text and ty
150. able with each group defined by a E PRIM column Vesen 6 0 ee Y i Cores Teats w Learn more Enter import data Ente rephcate values stacked into columns Ente pared of repeated masoures dats each subject on a seperate sow Ente aed plot enoi values ateady calculated elrewhere Erter Mean SD N xj Use sample data quency dalibution and hatogiam E thest Pared t test One sample Orsay ANOVA Decinary Oneway ANOVA Repeated measures ROC cuve Moie ampie data sets Clone a graph Graph portfobo Notes e To use Prism effectively you need to learn how to choose which of the six types of data table to select e Note the distinction between choosing sample data or creating an empty table into which you can enter or import data e Choosing the sample data for the unpaired t test only fills the table with data You ll choose an analysis in the next step 2 From the data table click Analyze and then choose the t test analysis Alternatively click the t test shortcut button above the Analyze button 1995 2014 GraphPad Software Inc s GraphPad Prism User Guide tE GraphPad Prism Projectl Unpaired t test data fe File Edit View Insert Change Arrange Window Help Prem Fle Sreet Unde Clipboard Anaine mm Ob 2 T x FF bel xte 9 00 Eme X plg miy Search results of D Date Tables I Unpaired t test data p Info Project info i Results S i Graphs E Unpaired
151. ac gestures Starting with release 6 0c and if you use Lion or later you can zoom Prism Mac by pinching with two fingers but only if that gesture is turned on in the Trackpad control panel You can also smart zoom by double tapping with two fingers Depending on where you tap that will zoom you in to see the entire page the graph plus all other objects on the page or just the graph 5 6 What if the toolbar or navigator is missing It is possible to use Prism without the Toolbar top and Navigator left and this can be useful on computers with tiny screens But it is easier to learn Prism 1995 2014 GraphPad Software Inc GraphPad Prism User Guide 5 7 with both the Toolbar and Navigator showing If someone else using the computer has turned off either it is easy to bring it back e If the toolbar is not showing on your computer drop the View menu and choose Main Toolbar e If the Navigator is not showing on your computer drop the View menu and choose Navigator e If the bottom toolbar is missing choose Bottom Toolbar on the View menu Opening multiple Prism files Distinguish multiple sheets in one project file from multiple files A Prism project can have multiple pages or sheets divided into five sections These are all saved in one Prism PZF or PZFX file Of course you can export individual data tables or graphs but this is not the same as saving the entire project as one Prism file People new to Pris
152. ad Prism Project1 Nonlin fit of Exponential decay W File Edit View Insert Change Arrange Window n A D 8 2 amp 2 x D YS Ae X nw 9 GB E Family Data with Results W Exponential decay Table of results One phase decay FEYO Plateau and al 1995 2014 GraphPad Software Inc 320 GraphPad Prism User Guide 16 2 Creating chains of analyses Results tables that can be analyzed further have green grids in contrast tables with red grids cannot be analyzed further There is no limit to how many analyses can be chained together in this way When you edit or update the data table Prism will update the entire analysis chain automatically Results LA Nonlin fit of Saturation Bindir LA Table of results nnanbseatcherd of Saturation Binding At the top of the Navigator you ll then see The Data with Results folder which shows results nested underneath the corresponding data tables Analysis chains appear as a series of indented sheet names In this example data are first transformed then normalized and then fit with nonlinear regression GF Data with Results B log dose vs response i F Transform of log dose vs response Go formalize of Transform of log dose vs response B Hs s Aonlin fit of Normalize of Transform of log dose iz Equation Table of results Curve STM attentions y ae nent asihe Aside aoh aanenette tan aasa aqt ard You can choose to hide
153. ake sense Graphing logarithms different than using a log axis A review of logarithms 15 3 1 What is a logarithmic axis A logarithmic axis changes the scale of an axis The two graphs below show the same two data sets plotted on different axes 1995 2014 GraphPad Software Inc Graphs Frame and axes 303 10000 e 100000 Ej z o LTT e 000 10000 Sooo tt 5 o e a e e e a 1000 e e 2 6000 a e e S EJ 2 e a 3 e pa a e 100 H g 8 p Ss e 4000 s m 10 e r 2000 e os e a e 1 s e e Arithmetic Geometric Arithmetic Geometric The graph on the left has a linear ordinary axis The difference between every pair of ticks is consistent 2000 in this example The graph on the right has a logarithmic axis The difference between every pair of ticks is not consistent From the bottom tick 0 1 to the next tick is a difference of 0 9 From the top tick 100 000 down to the next highest tick 10 000 is a difference of 90 000 What is consistent is the ratio Each axis tick represents a value ten fold higher than the previous tick The red dots plot a data set with equally spaced values Each dot represents a value with a Y value 500 higher than the dot below The dots are equally spaced on the graph on the left but far from equally spaced on the graph on the right To prevent overlap the points are jittered to the right and left so they don t overlap The horizontal position of the red do
154. ame and origin The frame determines the basic look of a graph and its position on the page 1995 2014 GraphPad Software Inc Graphs Frame and axes 271 Positioning a graph on the page Customizing a graph s frame and axes appearance Showing grid lines Setting the graph origin 15 1 1 Positioning a graph on the page If you plan to copy and paste the graph to another program or place the graph on a Prism layout you won t really care where it is on the page But if you plan to print that page you might care to position a graph precisely To see the position of a graph on the page Drop the View menu choose Zoom and choose To Fit Page This lets you see the entire page at once so 1995 2014 GraphPad Software Inc GraphPad Prism User Guide you can see the position of the graph relative to the entire page To center the graph on the page Click on the Center on page button in the Arrange section of the Prism toolbar Specific Binding fmol mg 0 0 25 50 75 100 125 150 Concentration 7 ICYP pM To specify an exact position on the page Click on the Format Axis tool in the Prism toolbar and enter the exact distance of the graph from the top and left edge of the page in the Frame and Origin tab of the Format Axes dialog Change P it ua al KON K d e amp 1995 2014 GraphPad Software Inc ia Format Axes Frame and Origin X anis Left Y anis Aight Y ais Titles amp Fonts
155. ame on each page as a header You ll probably want this header on pages placed in your notebook but not on graphs submitted for publication Print no grays and no colors Convert all colors to black Don t print colors as shades of gray Printing posters Prism can print on very large pages up to 1 5 by 2 meters so can create a poster directly If you use Windows 98 you will be limited to smaller page sizes Choose the paper size by dropping the File menu and choosing Printer setup Windows or Page Setup Mac The details vary with each printer driver Since you can only set the page size once for the entire project we suggest that you create your graphs in one project or several projects using a standard page size Then make your poster in a separate project created just for that purpose Set a large page size and then go to the layout section and create a layout sheet Arrange the placeholders and assign graphs from your other projects 22 4 Printing the gallery Open a Gallery page by clicking on the section title in the Navigator data tables 1995 2014 GraphPad Software Inc Printing m results graphs etc You ll see thumbnails of all the sheets in an array Distinguish two ways to print from the gallery Print selected sheets Select the sheets you want to print Then select the Print command or click on one of the Print buttons on the Prism toolbar Print the gallery page itself Click on the Print bu
156. an or equal to Here is an example Y IF Y lt Y0 Y Y Y If Y is less than YO then Y is unchanged Otherwise Y is transformed to Y squared Y IF lt 0 Y 0 Y This function returns Y if Y is positive or zero but otherwise leaves the results blank In other words it removes all negative values The way to leave a result blank is to do an impossible mathematical transform such as dividing by zero 18 3 Remove baseline Many kinds of data combine a measurement signal you care about with a baseline or background noise you don t care about You can analyze these data using two approaches One approach is to perform analysis on the total signal The other approach is to subtract or divide by a baseline or nonspecific value and then analyze and graph the results To access this analysis start from the data table click Analyze then chose the analysis Remove Baseline and Column Math 1995 2014 GraphPad Software Inc 352 GraphPad Prism User Guide Parameters Remove Baseline and Column Math heessa Definition of baseline Selected column s Every other data set column and 4th amp h v Assume the baseline is linear with X so use values predicted from the regression Ine Selected row s Calculation Difference Value Baseline Sum Value Baseline Product Value Baseline Ratio Value Baseline Percent 100 Value Baseline Fractional diference Value Baselne Baseline Percentage difference 10
157. and exporting data 159 Prism gives you several options to get data from other applications You can copy and paste or import 1995 2014 GraphPad Software Inc 160 GraphPad Prism User Guide 12 1 Key concept linking and embedding data When you copy and paste from an Excel file or text file into a Prism data table you have the option to paste only the values or to keep a live link to the original file so that whenever the original file is changed and saved your Prism graphs and analyses will update A third option is to embed keep a copy of the original file inside your Prism file When you link you keep a connection to the original file When you embed you make a new copy Linking and embedding works differently with Prism for Windows and Prism for Mac With Prism for Windows you can link or embed to Excel and text files With Prism for Mac you can t embed files or link directly to Excel spreadsheets You can however link to text files 12 2 Paste linking data from Prism Prism 6 offers a new feature You can copy data or results and paste link the data to the same or different data table You can either use the Paste Link command on the Edit menu and the right click shortcut menu or choose to link in the dialog that comes up when you choose Paste Special The pasted results are linked which means if the original data are edited or replaced the linked values will update too Example 1
158. and outer borders These setting are for all the segments of the graph Borders F Outer 2pe gt a Viirtemat 2pt a Titles Click to show or hide the graph title or to show or hide the total of all values The graph shows each category as the fraction of the total so it can be very useful to show the total near the graph With donut graphs it is common to put the total in the center of the graph as shown below Optionally add a prefix or suffix for example 1 000 Applicants or Total 1 000 Titles J Show graph title J Show totat Prefix Suffix Applicants Applicants for admission in 2011 55 43 567 Female Women 1023 Men Students 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 269 _ Order Reverse the order of the data sets to change the orientation of the graph 1023 Men Students Use the Size portion of the dialog to change the size of the whole of a donut graph Order Standard Reverse Women 1023 Men Women S tudents Size Urder Applicant fe eceission ia 2611 Diameter wesss Donut hole 15 Graphs Frame and axes The choices on the Format Axis dialog are self explanatory Don t overlook the Additional Ticks and Grid lines section which lets you place any numbers or labels anywhere on any axis And don t overlook the Frame and Origin tab Here is a list of shortcuts to change the axis directly without using the Format Axes
159. and saving Prism Files Commands Open filename Close Save lt filename gt Explanation Scripts can either be saved as part of a Prism file or in a separate script pzc file When the script is running from a separate file the Open and Close commands let you switch between Prism files The script commands work on the last opened file You may open several files at once To go back to a file you already opened simply reissue the open command again If you don t include a disk and directory Prism will look in the directory folder specified by the SetPath command Include the file extension PZF PZFX PZT or PZM Unlike the Import command the Open command by itself will not automatically open the next file file in a ForEach loop To do so use this syntax Open F PZF That opens the next file in the loop F with the extension PZF which you may want to change to PZFX The Close command does not save the file so issue the Save command first if you want to keep the changes Include a file name with the Save command to create a new file Omit the file name to save changes using the same name The Save command saves to either PZF or PZFX format depending on the file name you enter 1995 2014 GraphPad Software Inc 23 2 10 Importing data from a text file Commands Import lt filename gt lt row gt lt col gt lt subcol gt ImportLink lt filename gt lt row gt lt col gt lt
160. and the sqrt function takes the square root If you are transforming X values you may use Y in the function If the data table contains several data sets so has several Y values for a single X value Prism will stagger the results down the page repeating X values as needed The results for column A will appear on top of the results table Below that Prism will place the results for column B For these rows column A will be empty Usually the same function is applied to all data sets But you can write a transform to apply different transforms to different data sets To do this 1995 2014 GraphPad Software Inc Transforming normalizing etc 351 precede the lines that apply to only some data sets with column designators For example put lt B gt in front of a line in your transform that only applies to data set B Put lt A gt in front of a line that applies to all data sets except data set A Prism allows you to introduce some branching logic through use of the IF function The syntax is IF conditional expression value if true value if false You can precede a conditional expression with NOT and can connect two conditional expressions with AND or OR Examples of conditional expressions MAX gt 100 Ymax Constraint A lt B or A lt C NOT A lt B AND A lt C FRACTION lt gt 1 0 X lt A and X gt B Note lt gt means not equal to lt means less than or equal to and gt means greater th
161. aphs and layouts to the clipboard in the Preferences dialog Your only option is whether to include the page background Omit the background color if you will apply a fancier e g gradient background in another program EPS Like PDF EPS files contain vectors and fonts The resulting file isn t just an EPS wrapper around a bitmap file Prism Windows gives you thie choice of converting text to outlines glyphs If you do that the image will always look right no font files required but you wont be able to edit text in other programs If you include text as text it can be edited elsewhere but font files are required Prism Mac always converts text to outlines In theory the EPS format is the best tied with PDF It encodes everything as vectors and fonts so can be expanded or shrunk without any loss of resolution In fact submitting EPS files to journals is often problematic Fonts and EPS files JPEG The JPG format is designed for photographs with gradients of similar colors It is not a particularly good format for exporting for line art and graphs Prism offers this choice because some journals insist on it but we recommend that you use the TIF format when possible The only advantage of JPG is that the files are smaller Most programs that export to the JPG format give you a choice of compression If you compress more the files will be smaller but the resulting image won t be as sharp Prism gives you no choice It only
162. arts a new file called auto pzc and designates it as file number 1 The next 10 lines export Prism script commands you have written into that file The next line closes the script file which is launched by the final line shown above Further lines would import the results exported by Prism Putting all the commands into one file doesn t help conceptually You still have to distinguish the VBA code within Excel from the script commands of Prism The advantage is that you can do all the editing within one file rather than two The disadvantage is that writing the script is a bit harder as you have to place each line in quotations and precede it with Print 1 1995 2014 GraphPad Software Inc Putting Prism graphs into Excel In addition to importing the results of Prism analyses you may want to import a Prism graph into Excel Exporting the graph is no problem as a Prism script can export a graph or layout as a WMF picture The problem is importing it into Excel as there is no way to write Visual Basic commands to import a picture You can do it indirectly Create a picture object manually in Excel display the control toolbar click on the image button then drag to create the object Then write Basic code to change the contents of that picture object For example Sheet2 DRGraph Picture LoadPicture Path dr2 wmf 23 3 5 How long can a script be The maximum size of a script is not limited by number of lines but rather by
163. ass ccececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeneeeeaees 205 Changing a graph s Shape and SiZC ccccceeeeeeeeeeeeeeeeeee ee eeeeaaeeeeeeaaeeeeesaeeeeeeeaaeeeeesaaeeeeenas 207 Graphs Symbols bars lines and legends 210 XY graphs Formatting symbols and lines Appearance Of XY graphs sissies deini da eenaa Karain aa ainas aaa Aea raaa ada a eaat da neaei idiarena abie Front to back order of data sets nsss Use row titles to label data points NU AGING XY Gata S Ct icc ccisccclecvcecdcesdeseceticvcsece suet dncteciecbecheneevobecasescvedeccastersecdesschseubbichssessdsctsustedbectesenreisbisntersesters Additional XY Settings sisisi radiais ian eaaa aaraa adaa aa a aAa a Kaaba aaa Aaaah da daenda aiaiai Column graphs Bar formatting and Spacing ssssssssseusssrnennnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnn Appearance of Colm grap S isc icecciscescconssssensscsiecsedesssoscesscseasnesesstetatcecvedcedssssinesssvenscsubescazsezneuesisessnisesrasuereie Data set Spacing on Column Graphs ccecceeeceeeeceeeeeeeeeeeeeeaeeeeaeeeeaeeensaeeseaeeesaeeeesaeessaeeesaaeeneaeeseaeeeseeeensaeeesaees Pl tting order Of Column graphs icsiccccsssescasiedadeieiecedcteceesseccaseceaetecensdivstecesensesasesdusorsdusersieciesedeavenaeeseudnsersincers Additional Column graph settings Box and whiskers graphs FOP SE PlOts A caved cvczev sats sugaes cvectesnatvcsdeceusecusssveusessesscvenscncusevavecesessuy
164. at follows If the file doesn t exist yet Visual Basic waits 1 second and then loops back to test again whether the file exists Launching Prism from another program using OLE automation An alternative to the Shell command is to launch Prism using OLE or Active X automation Here is an example Set Prism CreateObject Prism command Prism SetPath C data july99 Prism visible Prism runcommand c prism5 doseresp pzc Prism quit Set Prism Nothing The first line creates a Prism command object You may give the object variable any name you like on the left side of the sign but it is convenient to name it Prism You don t have to tell the program the location of prism exe Windows takes care of this automatically via the registry The second line which is optional tells Prism which folder to use This replaces the need for a SetPath statement within the Prism script When running a script Prism looks for data files and templates in this directory folder first Place the name of the folder in quotation marks or use a text variable The third line tells Prism to show its progress dialog Once you have tested your code remove this line so Prism will run invisibly show no dialogs The fourth line launches the Prism script You must include the full path of the script file the directory used in the SetPath message above is not used auto matically 1995 2014 GraphPad Software Inc The final two li
165. ata and results tables Omit it for a cleaner look Print row and column labels When printing data tables print the row numbers on the left of every page and the column letters on top of every page Print the file name sheet name date and time at the top of every page Print the sheet name on each page as a header You ll probably want this header on pages placed in your notebook but not on graphs submitted for publication 22 3 Printing graphs and layouts Page orientation Each graph or layout can be portrait or landscape Since the page orientation setting in the portrait landscape setting of the printer setup dialog only allows one setting per file Prism ignores this setting for graphs and layouts Flipping the orientation of a graph 1995 2014 GraphPad Software Inc so GraphPad Prism User Guide Click the rotate button in the Change toolbar and choose Flip Change nile O KB we Flipping the page orientation does not change the aspect ratio of the graph You won t see the change on screen unless you zoom down to see the entire page Flipping the orientation of a layout Use the Flip button in the Change section of the Prism toolbar to change the orientation of a layout Change Printing preferences Two options shown on the File amp Printer tab of the Preferences dialog affect printing of graphs and layouts Print the file name sheet name date and time at the top of every page Print the sheet n
166. ata manipulations Choose X log X Also check the box at the bottom of the dialog to Create a New Graph of the results Prism will create a results table of the transformed data and a new graph To perform nonlinear regression on the transformed data click Analyze from either the results table or the new graph Plot data already entered as logarithms If you enter data as logarithms or graph the results of a log transform you should graph the data with a linear axis Don t choose a log scale Your data are already logarithms If your data represent logarithms you can format the axis numbering to make this clear 1995 2014 GraphPad Software Inc Graphs Frame and axes 313 r Format Axes s Frame and Origin X axis Leit Y ads Right Y axis Titles amp Fonts Gaps and Direction Standard Scale Log 10 l Y Automatically detemine the range and interval Range Mirman 0 001 Maximum 10 All ticks Ticks drection Down X Location of numbering labeling Below horizontal v Ticks length Short X Numbering labeling angle 0 Regularly spaced ticks Major ticks intervat 1 0 powers of 10 For Log A decimal places Starting at lt 0 001 Thousands Andog Minor ticks 9g mem Fg Prok oe Additional ticks and grid lines AtK Tick Lie Text Fonts Greek Details Show additional ticks With reguar ticks Instead of regular ticks Only regular ticks He Cance aoe C ok
167. atically G Y intersects the X axis at X X intersects the 1 61 in Wide gt 526 n Size Distance of Y axis from left edge Width Length of Xx axis Distance of axis from bottom edge 276 in Set the default size and shape for new graphs Pull down the Edit Preferences menu and from the Graph tab choose Wide Tall or Square On a wide or tall graph the long axis is 1 5 times the length of the short axis Preferences media Into Sheet Fite Locations _ Send to MS Office View Fie amp Printer NewGraphs Analysis Intemet Axes Defauk color scheme Height 200 Black and white gt Fonts Frame No frame X Man Title Thickness 1 mares We z AvisTitles Ticks Outside X Numbenng Enor Bar Style T Legends amp Labels Thickness 2p Embedded tables Row Titles Make a graph larger or smaller including fonts Click the Resize Graph button in the Change section of the Prism toolbar This button enlarges or shrinks both the graph and also the graph s symbols and fonts In contrast resizing by stretching an axis doesn t change symbol or font size 1995 2014 GraphPad Software Inc Prism Graphs the basics 209 Change Arange Draw mil a A OA IMr A A Smaller Larger To Fill Page More Choices If you click More Choices a dialog lets you pick the exact size you want and lets you resize the gra
168. ause there is no need to store the data and settings this approach doesn t take up so much disk space Paste a graph or layout as a link Prism can paste a picture along with a link to the Prism file When you double click Prism will be launched and open the linked Prism project You can then edit the data analysis settings or graph in Prism When you exit the revised graph will be updated in Word or PowerPoint One advantage of this method over pasting an object is that your Word or PowerPoint files will be smaller Another advantage for some is that it keeps your data in one place for easy editing The disadvantage is that the link really is just a link to a file with a particular name in a particular place If the linked file has been deleted renamed or moved you won t be able to edit it If you move the Word or PowerPoint to another computer you won t be able to open the linked file unless it too is moved Insert object If you insert a Prism object into Word or PowerPoint you ll embed an entire Prism project In contrast when you paste a graph as an object you only 1995 2014 GraphPad Software Inc Exporting images from Prism o embed the data and results linked to that graph Choose the Insert Object command from the other program s Insert menu or in Office 2007 the right side of the Insert tab Choose to create object from a file and choose your Prism file The advantage of this method is that it include
169. ave and recycle templates Navigation tips View all sheets in the gallery Click on the Data Table Info Results Graphs or Layouts folder name in the Navigator to open the Gallery Or click the Gallery button on the bottom toolbar 1995 2014 GraphPad Software Inc eo GraphPad Prism User Guide The gallery shows all sheets in a section Double click on the one you want to go to Or select several sheets to work on at once IF GraphPad Prism area under curve pzf Data 1 graph oj TA File Edit View insert Change Arange Window Help Prism File Sheet Undo Clipboard Anslyss Change Arenge Oww Verte Text PS D B 2 Kk ni lE ki Q SE Xwe Qe Bane ti A E iie Be 3 Family J Search results Data with Results D i Data 1 i lt we a Osta Tables i Il info Project info J Results B Graphs k Data 1 graph V Data 1 graph Transform of Data 1 graph Normalize of Transform of Oat kA Transform of Data 1 grap l Normalize of Transform B Layouts jis Layout 1 ub Floating Notes EEEE con upauan Jump between related sheets using the Family folder Open the Family folder to see all sheets linked to the current one Or click the Link button in the bottom toolbar to jump to one of those linked sheets 2 O info D O Results O Graphs O Layouts GQ Floating Notes q 1 DOSE gt gt a0 Ulu Trace an analysis chain using the Data with Results folder Open the Data with Results folder to t
170. aveutedusevesssiunsvevetersvenesvsciseseets Grouped amp contingency graphs Symbols and line formatting Appearance of Grouped and Contingency graphs cccsccccsecceeeeeeeeeeeeeeeeeseeeesaeeeeeeeesneeesaeeeeeaeeeeeeensneeees Data set grouping and spacing on Grouped graphs Plotting order of Grouped graphs cescceseeceeeeeeeeeeeeeteee Additional Grouped graph settings Row or Column titles UNder Dar cecsseeesseeeeseeneeeeseaeenenseeeseseenseeseeeeseesneeseeeseeesseeseesseneesesaeeeseessenseesneenenes 257 Survival graphs Formatting Options cccccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeaeeeeeeeaaeeeeseaaeeeeeeaaeeeeenes Appearance of Survival graphs c cccsccecseeeeeeeeeeeeeeeseeeesneeeeseeeeseesnsneeesaeeessaesesnesesaeeeeseeeeseaeesaeeeseeeenseeenseeeees Changing the plotting order of data sets 1995 2014 GraphPad Software Inc 6 GraphPad Prism User Guide 5 Part XV 1 3 Part XVI oN Oa FPF WN Part XVII 1 2 3 4 5 Part XVIII N dgin S rvival data Sets ds ae a areae evens aaae AE A hey enced sessaseciav scce snes aia 264 Parts of whole graphs iiss cca seeg edie siete decdeneccceeetbscotveedsdieue tbs decueed Scceustedecepeedsdeesvebs ceovesdcccevsebhe 266 Graphs Frame and axes 269 FraMe ANG Origin saarnia eeina draa canes asda cecadsevebsetindacecebespaceuundadevecscaaesuitedsetebvasayeer 270 Positioning a graph on the page cc ccceseceeseeeeseeeeeeneeeseeeeeaeeeeane
171. axis to open the Format Axes dialog and set the number format in the Numbering or Labeling section Choose Equal or Log spacing and the number of intervals you want between major ticks not the number of ticks 1995 2014 GraphPad Software Inc 306 GraphPad Prism User Guide Format Axes me Frame andOrign Xass Left Y axis Right Y axis Tiles amp Fonts Gaps and Direction Standard Scale Log 10 v Automatcaly determine the range and mterval Range Minimum bal Maximum 10 ma All ticks Ticks direction Down X Location of numbering labeling Below hoizota Ticks length Short x Numbenng labeling ange Regularly spaced ticks Major ticks interval 1 0 powers of 10 Format Log decimal places Staring amp X 1 Thousands 100000 Minor ticks 9 rmm z log Prefix Suffix Additional tick dditional ticks am At X 3 mr Text Fonts Greek Detais Show additional ticks ee Ga With regular ticks 5r Instead of regular ticks 6 wre morm Oriy regular ticks 8 moror poeeme Heb Cancel Apply 15 3 3 Logarithmic axes cannot contain zero or negative numbers The logarithms of negative numbers and zero are simply not defined Let s start with the fundamental definition of a logarithm If 10 Z then L is the logarithm base 10 of Z If Lis a negative value then Z is a positive fraction less than 1 0 If Lis zero then Z equals 1 0 If L is greater than O then Z is greater than 1 0 N
172. ayOut ccccceeeceeeeeeeeeeeeeeeeeeeeeeeeeeeee ee eeeseeeeeeseeeeeeeeseeseeeeeeeeeeeeseneees 364 6 Creating a depth Chart wicicicciccciiscecesccssiececsccevecccceeeeeescteweieedeeeeed seceeedveceeeevessteeieesctevedseeeeeds 366 7 Master legends one legend for several Qraph cccececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeneeeeeeeneees 369 Part XX Adding text drawings and pictures to graphs or layouts 370 1 Adding te Xt isniciicccecacccce sive sececenecscunweasadeeede catentvescdeeeee sbbest a cibenseeeb cunts sdeeetenecuiteasadvineesncunts 371 2 Using Word to add text Windows ONy cccceeeeceeeeeeeeeeeeeeeeeeeeeeeeeesaeeeeeseaeeeeeesaeeeeeseaneeeees 374 3 Drawing lines arrows ANd SHAPES 0ccceeeee cece eee eee eee ee eee eee eee ee eeee see see seeeeaeeeaeeeaeeeeee 375 4 Including pictures and other ObDjects cccececeeeeeeeeeeeeeeeeeee seen eeeeeeeeeeeeeeeeeeeeeeneeseneeeneneees 376 5 Tips for Moving Objects ArOUN ccceeeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeseeeeeeneees 377 6 Aligning objects on a Qraphh cececceecceeeeeeee ee eeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeeeeeseeeeeeeeeeeseeneeneneees 379 Part XXI Exporting images from Prism 382 1 How to export one or more graphs Or layOUtS cceceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeneeeeneeees 384 2 Expono Opi HS soc seeeacie cies fade cee cet cau ope sec wedded Sadie r Aaa a Ae aar EENES E 384 3 The differences between export formats
173. bles gi Data 1 S Info p Results LA Normalize of Transform of Data 1 graph E Leyouts layout Jl Floating Notes transform of Gets 1 graph Working with several sheets at once Many commands are available that work on all selected sheets at once Right click on the gallery to see a list of all available commands e Print each selected sheet separately or print a combined gallery page 1995 2014 GraphPad Software Inc Organizing Prism projects 83 in z E Piintar Name Microsol XPS Document Writer X Properties Status Ready Type Microsolt XPS Document Wiiter where XPSPort Coumark Prir to file Print range Copies Entire Project N mon 1 Sheets from 1 to 3 Current Sheet 3 liste Selected Sheet Galey gt Options e Export e Send to Microsoft Word or PowerPoint e Magic Make graphs consistent e Apply a color scheme e Change the background color or plotting area color e Rename Add a prefix or suffix to their existing names or give all selected sheets the same name followed by 1 2 3 Rename Selected Sheets erlace with new name followed by 1 2 New Name Experiment 4124 Prefix or append to existing names Prefix sheet name with Append after sheet name 1995 2014 GraphPad Software Inc e GraphPad Prism User Guide 6 3 Freezing a sheet to prevent changes When you edit data Prism automati
174. cally recalculates the analyses and updates the graphs Freeze a results or graph sheet if you don t want it to update For example you might want to freeze results and a graph before excluding some outliers from the data You can then repeat the analysis and have both copies of the results and graphs in the project Note that Prism doesn t let you freeze data tables info sheets or layouts Click the Freeze button in the Sheet section of the Prism toolbar to freeze a results sheet or graph The Prism bottom toolbar will indicate that the sheet has been frozen and won t update with any changes to the data Click again to unfreeze Sheet X J New Ee BS CFrozen gt 6 4 Using Info sheets to organize your projects Key concepts Info sheets e Use Info sheets to record experimental details and constants you want to use in analyses e The left side of an info sheet is a table of structured information The right side is for unstructured notes e Each project can have up to 500 info sheets Each Info sheet can be linked to a particular data table but doesn t have to be e The info constants can be used hooked in analyses 1995 2014 GraphPad Software Inc Organizing Prism projects 85 Create and edit an Info sheet To create an info sheet click the New button on the toolbar or drop the Insert menu Choose New Info Select whether the new sheet should be linked to a particular data table or a global Info shee
175. cccccceceeeeeeeeeeeeeeeeeeeeeeeeeeaeeeeeeeaeeeeeeeaeeeeeeeaeeeeeseas 183 Exporting from data tables ccccceseeceeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeseaeeeeeeaeeeeeesaeeeeessaneeeeesaneeeees 186 Prism Graphs the basics 190 Creating Qrapns viciciicciccisescseccsiavenetiesaneccse eveeetiessteucte a veeetbesibetcaeaveentbe saiecceiaseeetbesadetceiaveentii 192 The Format Graph dialog seseina inanar eian i annA EE cenedeaeacecegesdectaesviepeeneyceteaees 192 The Format Axis dialogoan anren iaeiae laikaa aaae aian siaaa sued cceeyecbiaeraewioceeveents 194 Changing the type of graph ic ccececcccctecccccteneectecteieiecteeeeceeesehenectneecteeleisnectevecteueceienstteneectoe 195 Changing which data are plotted ccccceeeeeeeeeeeeeeeee nese ee eeeeeeeeeeeeaeeeeeeeaeeeeeeeaaeeeeeeaaneeeeees 195 Prism Magic Make Graphs Consistent cccceeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeesaeeeeessaeeeeessaneeeees 197 Color She Me Sik cciccsiteccccissscectstaseecctessebeteesseeeccuaspeutecasenectes eebeutedseneedeesveueedadeemetessventicdeeenets 199 Selecting Colors MaC cci ci ccccscccccctaceecencsceexcbedewsdewadcvesdabecweseccadyexctndewsyencdeverdabecyssecdecyeretuce 201 Selecting colors WiNdOWS icccsce ccc csevciecssee deen thensadenceeccuueterscecdswedceuceenenccneeeeceueteverssacberetues 202 Rotating flipping reVErsing ccccceeeeceeeeeeeeeeeeeeeeeeeeeeeeeesaeeeeeeeaeeeeeeeaeeeeeesaeseeeesaeeeeeesaneeeees 203 Formatting individual symbols and D
176. cheme command 424 Arithmetic series inserting 143 Arranging objects 379 Arrows 375 Assigning graphs to a layout 362 Audio notes 87 Autocomplete 131 133 Automatic backups 103 Automating with scripts 419 Automating work 326 Automator 441 1995 2014 GraphPad Software Inc Axes origin 277 Axes logarithmic 307 Axes offsetting 273 Axis limits 279 Axis numbering 280 Axis titles 298 Axis hiding 286 Pe Backing up Prism projects 103 Backup preferences 89 Backups 103 Bar graphs don t use log Y axis 310 Bar graphs which table 124 Baseline removing 351 Batch processing Prism Magic 197 Beep command 438 Blue italics outliers 139 BMP importing 376 box and whisker plot 237 Box around graph 273 Boxes 375 boxplot 237 Bring to back 379 Bring to front 379 sO Cadmus 389 Center on page 271 Chained analyses 71 Chaining analyses 320 Change all data sets 192 Changing a data table format 122 Changing analyses 321 Changing decimal places on data table 138 Changing graph type 195 Changing subcolumns on data table 122 Changing Xto Y 355 Characters 376 Circles 375 Citing Prism 461 Clear background 394 ClearTable command 424 Clone a graph 94 Cloning a layout 359 GraphPad Prism User Guide Close command 426 CloseOutput command 433 CMYK vs RGB 391 Color models 391 Colorschemes 199 Column datatables 115 Column math 351 Column titles 131 Column wdiths 137 Combining projec
177. ck on the Prism desktop icon and In Properties change the target to add the command after the last quote mark Leave a space between the quote mark and the slash so the target looks like this C Program Files GraphPad Prism5 prism exe U You can use hyphens or slashes U and U interchangeaby All of the options shown below also work if you use the Shell command to launch Prism from another program using Visual Basic for Applications VBA These options only work on Windows There is no similar mechanism for sending startup commands to Mac applications Run prism script some_prism_script_file_path To create an icon that launches a specific Prism script point your mouse to an empty spot on the desktop click the right mouse button and select New Shortcut Enter a command line that starts Prism and points to the Prism script file to launch Include the symbol in front of the path to the script name If either path includes spaces include the entire path in quotes as shown below C Program Files GraphPad Prism5 prism exe c program files GraphPad Prism5 scri 1995 2014 GraphPad Software Inc as GraphPad Prism User Guide Turrning off check for update U When Prism Windows first starts it tries to check for updates via the web If it can t connect it normally just keeps going But in very rare cases it tries to check for updates and then can t get past this step so never gets to the Welcome dialog T
178. ction to specify each label and its location X coordinate Check the option to plot only these additional ticks instead of regular ticks E Format Axes es Fiame and Origin X axis Lett Y axis Right Y axis Tiles amp Fonts Gaps andDirection Standard gt Scale Lines v Automatically determine the range and interval Range Minimum Re Maimun All ticks Ticks direction Down 7 Location of numbering labeling Below angled al Ticks length Shot Numberng abeling angle 45 Regularly spaced ticks Starting at 0 Decimals Auto gt Suffix Mince ticks mn r bg Thousands 10000 Additional ticks and grid lines Forts Greek Detale a Show additional ticks With regular ticks Instead ol regular ticks 5 Only regu ticks Help Cancel Apply OK 1995 2014 GraphPad Software Inc 302 GraphPad Prism User Guide 15 3 Logarithmic axes If your data span a wide range of values it can be easier to visualize the results when you make one of the axes logarithmic Distinguish between transforming your data to logarithms which creates a new results table from choosing a logarithmic axis which only stretches the axis without altering your data What is a logarithmic axis How to Create a log axis Logarithmic axes cannot contain zero or negative numbers Regression fits the data not the graph When to use a logarithmic axis Advice Bar graphs with log axes rarely m
179. d these will be used during that session But those changes won t get saved and so won t be seen by the next user How to prevent saving changes to the preferences file Mac When Prism is used in a teaching lab you want Prism to startup the same way each time When a student uses Prism you don t want preferences set by other students to be used as that would make it seem that Prism acts unpredictably The method explained above for Windows doesn t work because there are no command line switches in OSX Instead create and write protect the preference file 1 Delete the Prism preference file com GraphPad Prism plist from local user Library Preferences 2 Launch Prism so it creates a default preference file 3 Set any preferences as you want them to appear for each user Also create any color schemes or user defined equations you want everyone to access 4 Quit Prism 1995 2014 GraphPad Software Inc Standardizing Prism use in a lab s 5 Write protect the preference file Open the folder that contains the preference file local user Library Preferences Beware that Macs have multiple Library folders Pick the one within the local user that each student will log in as not the overall Library folder Right click on the file com GraphPad Prism plist and choose Get Info Check Locked Repeat for the file that contains the list of autocomplete text entries com GraphPad Prism autocomplete plist 24 2 Indiv
180. d press Update to close the dialog To unlink a data object Double click anywhere within the object to bring up the Import and Paste Special dialog Click the Unlink button on the bottom of that dialog The values will remain on Prism s data table but will no longer be linked to an external file or to an embedded spreadsheet 1995 2014 GraphPad Software Inc 184 GraphPad Prism User Guide To move a data object to a different location on the same table Double click anywhere on the data object to open the Import and Paste Special Choices dialog Go to the Placement tab Find the spot where you can change the top left corner of the object Enter a row number and choose a column for the new location To move a data object to a different data table It is not possible to move a data object to a different data table You can delete it from the table where it doesn t belong Then go back to the source data and copy paste special to the correct location To update values in Prism after editing a linked file Double click on the data object in Prism to bring up the Import and Paste Special dialog Press the Update button on that dialog This is only necessary if you didn t check the option to automatically update on the Source tab To change the region of a spreadsheet file linked to Prism Windows only If you accidentally linked to the wrong part of a linked spreadsheet the simplest approach is to unlink the data object
181. d 36 41 4 98 87 95 99 8 2 Normal culture 19 26 29 2 32 29 26 33 3 3 Here are the data plotted as an interleaved graph 150 Wild type cells m VVTC911 cell line 100 50 0 42 sS s 5 Vo amp D g amp o You can also choose to superimpose the groups 1995 2014 GraphPad Software Inc Data tables 131 150 100 50 Serum starved Normal culture 10 6 Column titles Why use column titles Column titles are used to e Identify data sets on a data table e Identify data sets when choosing analyses and viewing results e Labeling the X axis of Column and sometimes grouped graphs e Creating legends for XY and Grouped graphs Enter two or three line row titles and column titles You may enter two or more lines of text for each column title This is new to Prism 6 You may also now bold italicize and underline text in titles you could always use superscript subscripts and Greek 1995 2014 GraphPad Software Inc 132 GraphPad Prism User Guide Group A Group B 3 Control Treated with Antagonis Data subset 1 To add an additional line of text to the title click the Line Break symbol or press the key combination Shift Enter to move to the next line XML a View and edit all the column titles at once To view and edit multiple column titles at once click on the Format Data table button in the upper right corner of the data table and choose the tab for column titles If your
182. d Agonist Psummary Solvent Blank ns Significant Treated Yes Significant Treated Antagonist No Significant Treated Agonist Yes Significant Solvent Blank No 1995 2014 GraphPad Software Inc as GraphPad Prism User Guide Example 4 WTBlock 7 7 3 4 Treated Treated Antagonist Treated Agonist Solvent Blanks Yes No Yes No kkk Ns ns Example 5 WTBlock 7 3 Significant Significant v Ne v Ne Prism file 23 2 19 Send to Microsoft Office Commands SendToWord SendToPP Explanation These commands send the current graph or layout to Word or PowerPoint 23 2 20 Special purpose commands Commands SetProjectName new name SetScriptDialogTitle dialog title RecalcAll Beep 1995 2014 GraphPad Software Inc Createlog SetSheetTitle hew_name lt K gt CloseScriptDialog Print Exit Explanation Use the SetProjectName command to change the name of the project file the name it will have when next saved and the SetScriptDialogTitle command to change the wording of the dialog that shows while the script is running only useful if you are creating scripts to be used by others If you are opening a file created by a prior version of Prism and saved in the large format which includes analysis results the RecalcAll command will tell Prism to recalculate all the results If you script takes a long time to complete you might want to use the Beep command to alert
183. d Software Inc 25 GraphPad Prism User Guide Baseline Automatic Bars beginatyY 100 Hide baseline 2500 2000 1500 GB dogs EB hopes 1000 500 0 i Red Black Yellow Dimensions Use this setting to set adjust the spacing between columns on a graph To make the columns wider make the spacing smaller Spacing as percent of space used for data Between adacert data 50 Additional gap between groups 100 Red Black Yellow Red Black Yellow When a bar value is zero Choose whether or not you want a space for the bar where the zero value is dogs on the graphs below When a value is blank Create a zero heigtt bar Dont leave a gap Red Yellow Discontinuous axis When you have a gap in a Y axis choose whether or not you also want a gap 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 257 in any columns that span the gap Not leaving a gap may make your graph misleading Discontinuous axis When the axis is discontinuous also make the bars or connecting ines decontinuous me To mo Red Black Yellow 14 3 5 Row or column titles under bars You can change how the bars are labeled Double click on the axis to bring up Format Axis then choose to use Row numbers Row titles or Column titles pan Format Axes Frame and Origin X axis Lett Y anis Right Y anis Tiles amp Fonts Gaps and Direction tandard Scale
184. d table see below and use only the top row i as Group A Group B Grouped 4 x Mean SD Mean SD N 1 Grouped graphs Each column represents a different kind of bar Each row is a different instance of that bar Enter replicates if any in side by side subcolumns So if you have three Y columns and four rows you will have three kinds of bars and you can choose the color fill and border of each You will have four different bars of each type You can choose whether you want the bars interleaved stacked or separated on the Welcome dialog or by clicking Change and then Type of graph 1995 2014 GraphPad Software Inc 126 GraphPad Prism User Guide Data 3 EE Cats mm Dogs gt Hamsters x Contingency tables A contingency table is like a grouped table but doesn t have subcolumns for replicate values Table format 4 1 PLacebo 2 Aspirin 3 Title Prospective aspirin and Ml 15000 GB Myocardial Infarction Eo M 10000 5000 Placebo Aspirin XY Bar graphs 1995 2014 GraphPad Software Inc Data tables 127 Both the kinds of bar graphs mentioned above place the bars on the graph in order with equal spacing In some cases you want to position each bar along the X axis with the position determined by an X coordinate you enter To make this graph choose the Spikes graph in the New Graph dialog X Days A x x 238 Title 239 Title Table fo
185. data tables In an XY table every point is defined by both an X and a Y value Analyses performed with XY data e Linear regression e Nonlinear regression e Correlation Pearson or Spearman e Cubic spline amp LOWESS e Smooth curve e Area under curve Example of an XY table Table format X Group A Group B xY Seconds Control Treated A Y1 A Y2 A Y3 B Y1 B Y2 B Y3 35 31 4 36 39 25 43 49 50 57 67 87 89 6 77 89 9 102 145 15 145 121 254 269 231 167 187 14 289 296 271 e Each row defines an X value Each column defines a treatment group Subcolumns are for replicates in a treatment group Prism uses these to calculate error bars Blank cells represent missing values Blue italics values are excluded from graphs and analyses Row titles can be used to label individual subjects or samples An XY data table can contain 256 data set columns and as many as 256 sub columns e There can be only one X column per table Error bars Prism will compute and graph error bars from replicate values placed in side by side subcolumns as shown triplicate values in the table above Specify the number of subcolumns when you create a new XY table You can also choose to create subcolumns formatted for entry of error values computed elsewhere 1995 2014 GraphPad Software Inc ma GraphPad Prism User Guide eee X Group A Group B xY x Mean sD N Mean SD N EEEEEE Prism can also plot horizontal X error bars
186. de axes Show both and Y C Show Scale Ba Margid None Minor gid None Colce Ate X Color Ate Thickness 7 pl Thickness 1 2 pt Style Style 15 2 Axes Scientists often individualize the axis range numbering and ticks Axis range Axis numbering Major and minor ticks Graphs with two Y axes Hide an axis and show scale bars Put a gap in an axis Additional ticks and grids Axis titles 1995 2014 GraphPad Software Inc Graphs Frame and axes 279 15 2 1 Axis range Double click on an axis to open the Frame and Origin tab of the Format Axes dialog Or click on the Format Axis tool in the Prism toolbar Change P it aa al KAN KW e amp Prism chooses the range of each axis automatically To override this uncheck the Automatically determine the range and interval box and enter the minimum and maximum value you want plotted on the axis You can also hook a range limit to an info constant 1995 2014 GraphPad Software Inc 280 GraphPad Prism User Guide a Friar Aen Er axis Left Y axis Right Y as Titles amp Fonts Gaps and Directors Standaed Scale V Automatically determine the range and interval Minimum a0 Too All ticks Ticks Grectiorc Lett Short Regularly spaced ticks Ticks length Decimal Format Mar ticks ntervak 100 0 x Auto gt decimal places Starting at Y Thousands Minor ticks tree Prefec Add
187. default Full page width rine Left side of page floating wrap text on the right Aight ade of page floating wrap text on the left Graph or layout colors in Word Ful colos same as in Prism Monochrome black and white no gray Grayscale Border within woed Draw a box around the graph No box Note These options apply when you use the Send to Woerd or Send toPowerPort command or buttons but do not apply when pou copy and paste The most important choice Windows only is whether to embed link or send a picture Embedding is the most versatile but makes your Word or PowerPoint files larger When sending to Word choose whether to display full colors black and white or gray scale The latter two options simply set a setting within Word to display and print the graph in black and white or gray If you embed or link and double click to edit in Prism you ll see the graph in its original colors Problems sending to Word or PowerPoint EMF vs WMF Windows supports two similar formats for describing images using vectors and fonts The WMF Windows Metafile format is older The EMF Enhanced metafile format is newer and in theory a bit better In fact one format works better for some programs and the other format for others It seems impossible to predict By default Prism places both formats on the clipboard and lets the pasting program decide which one to use Because some programs make the wrong
188. der versions of Prism you were able to define this series at the time you created the table With Prism 6 you can no longer do this You must first create the table and then use Format Data Table to define the series e When you define the X axis to be a series Prism will delete any X value you had entered into the X column without asking for confirmation e With this method the entire X column becomes a nearly infinite series You cannot tell Prism where to stop the series e With this method the series is always arithmetic each value is computed by adding a constant increment to the prior one Use the Insert Series dialog to create a geometrical series each value is computed by multiplying a constant factor times the prior one 10 15 Rounding Numbers entered with many digits When you enter data with more than seven digits Prism will store only seven actually it is binary so it is about seven decimal digits so will not store the exact value you entered For example if you enter the value 99 2492427 into a data table Prism rounds it to 99 249250 Prism stores numbers with single precision so it can only store about seven significant figures If you enter more Prism rounds off The conversion from decimal to binary and back means that the rounding is not always what you d predict Numbers entered with seven or fewer digits The problem of rounding Rounding values is straightforward unless the next digit is 5 Should
189. des of A B C etc The sum of the five values in the table 61 is the total number of students Table format a Parts of whole Number of Students x Y a on el wn b iim olojo gt You can enter data onto as many columns as you want But note that only the values entered into column A will be automatically graphed Use New Graph to plot other columns 10 Data tables 1995 2014 GraphPad Software Inc Data tables 121 Unlike Excel or most other graphics programs Prism s data tables are formatted In most cases the first column is for X The rest of the columns are for Y values and these can be divided into subcolumns for entry of error bars 1995 2014 GraphPad Software Inc 122 GraphPad Prism User Guide 10 1 How to create a new data table A Prism project can contain many data tables Click the new button from the Sheet section of the Prism toolbar or drop the Insert menu and choose New Data Table and Graph Sheet 2ER x The New Data Table and Graph dialog looks a lot like the Welcome dialog with fewer choices Choose which of six kinds of data tables you want and whether to start with an empty table or use sample data If you choose to create an XY or Grouped table and are not using sample data you ll also need to decide about subcolumn format 10 2 Data table limits You can have up to 500 data tables in your project Each data table can contain e Any number of rows limited by R
190. dialog Use the Graph Settings tab of the Format Graph dialog to change the direction of bars on a graph from vertical to horizontal to set the baseline for graph columns and to adjust the space between columns Double click on any bar to open the dialog 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 235 7 Format Graph Appearance Data Sets on Graph Graph Settings Direction Vertical Horizontal Baseline Automatic Bars begn a Y F Hide baseine Dimensions Space between columns 50 of cokmn width Discontinuous axis When the axis is discontinuous also make the bas connecting Ines dscontnuous Format of individual bars To format 4 bar differently than the rest exi thes dialog right cick on the bar and choose Foemat This Bar Remove all the individual formatting Revert all bars to the format of their data sets aD oe a Rotate columns from vertical to horizontal co ed 40 J30 20 cH H PKR H SH You also can use the Rotate button Aile ES ABS Baseline e Fill in this box to change the baseline for bars on a graph The default is for the bars to begin at the X axis 1995 2014 GraphPad Software Inc 236 GraphPad Prism User Guide Baseline Automatic Basbegna y 100 F Hide baseline 180 160 140 120 100 80 60 40 20 S r E s A e Check the box for Hide Baseline if you want your bars to
191. dian of the two groups That is not precisely correct as it is possible for two groups to have the same median but for the Mann Whitney test to find that the difference between the distribution of ranks among the two groups is statistically significant However if you assume that the two distributions have roughly the same shape then it is fair to think of the Mann Whitney test as comparing two medians Accordingly Prism 6 can now report the confidence interval for the difference of two medians The Wilcoxon test computes the 95 CI of the median The Wilcoxon matched pairs test nonparametric test of two paired or matched groups reports the confidence interval of the median of the paired differences and the Wilcoxon signed rank sum test nonparametric test to compare a median with a hypothetical median now reports the confidence interval of the difference between the actual sample median and the hypothetical median Ratio t test The paired t test works by analyzing the difference between each pair of values testing the null hypothesis that the average difference is zero With some kinds of data the difference between before and after is not a consistent measure of effect The differences might be larger when the before values are larger and smaller when the before values are smaller The ratio after before may be a much more consistent way to quantify the effect of the treatment Actually it turns out that analyzing the logarithm
192. dobe products offer a third way to deal with fonts that combines the best of the two approaches above The font definitions themselves are included in the file so the text remains as text but will render perfectly on any computer As far as we can tell this choice only works within Adobe products and Adobe has not provided the hooks our programmers would need to implement this approach Beware of the phrase embedding fonts as it is not used consistently Adobe uses it to describe the third approach listed above including font definitions in the file Prism 5 and earlier and some other programs use the phrase embedding fonts to mean the second choice above converting fonts to outlines or glyphs 21 7 The size of exported graphs and layouts How to change the size of a graph in Prism When exporting a graph to submit to a journal you will often want to set the exact width of the graph and any other objects text legends drawing pictures results tables on the graph page There are two ways to change the size of the graph in Prism e Set the width of the exported graph on the Export dialog e On the graph page Drop the Change menu and choose Resize Graph A third possibility is to change the length of the X axis in the Format Axis dialog But just sets the axis length The full graph will be wider when you consider titles numbering legends drawing etc We recommend the second approach above change the size of the graph in
193. does not fill the screen e Hide the Prism Navigator tree To hide the navigator use a command in the View menu or the leftmost button in the bottom toolbar Fe EB e Hide the main top toolbar and use the menu commands instead To hide the toolbar use a command in the View menu You can also hide the bottom toolbar but we suggest you don t If you hide the 1995 2014 GraphPad Software Inc GraphPad Prism User Guide navigator you ll want to use the bottom toolbar to navigate from sheet to sheet and section to section 6 Organizing Prism projects 1995 2014 GraphPad Software Inc Organizing Prism projects A Prism project file or PZF file contains all the pieces of a project Each Prism project has basic five sections Data tables Info sheets Results Graphs and Layouts Each section can have up to 500 sheets The term sheet refers to an individual data table info page set of results graph or page layout 1995 2014 GraphPad Software Inc so GraphPad Prism User Guide 6 1 Renaming sorting and deleting sheets Prism initially assigns each data table a generic name such as Table 1 It is easier to manage large projects if you give the sheets more descriptive names change their order and delete unneeded sheets To rename any sheet in a Prism file Click on the name of the sheet in the Navigator and press F2 or wait for a second and then click again to rename the sheet Or righ
194. e The link is live so will be updated if the data are edited or in some cases if the analysis parameters changed You can also hook constants entered on an Info sheet Which analysis results can be hooked Here is the list of all analysis results that can be hooked Analysis Values that can be hooked Nonlinear e Best fit value of each parameter regression e Lower confidence limit of each parameter e Upper confidence limit of each parameter 1995 2014 GraphPad Software Inc Analyzing data with Prism 3z Survival e Median survival analysis Bland Altman e Bias Lower 95 confidence limit of bias e Upper 95 confidence limit of bias Column e Mean with lower and upper confidence limits statistics e Geometric mean with lower and upper confidence limits e 25th and 75th percentile e Median e Lowest value e Highest value e QC control lines Mean plus or minus 1 2 or 3 SD e SD e SEM e N e Sum You cannot add to this list but we can so send us suggestions How to hook You ll see hook icons on many dialogs next to fields requiring you to enter a value Click and then choose an analysis constant or info constant on the Hook dialog 1995 2014 GraphPad Software Inc 32 GraphPad Prism User Guide Choose a value from an info analysis constant This will be hot ink to be automatically updated in the future ES Nonlin fit of Normalize of Transform of Dose response data BB no in
195. e a graph or layout as a Prism object 1995 2014 GraphPad Software Inc so GraphPad Prism User Guide Prism will paste a picture of the graph plus a copy of all the data analyses and graphical settings needed to create that graph or layout Double click the object in the other program to edit it within Prism where you can edit data change analysis settings and format the graph When you exit Prism the revised graph will appear in Word The advantage of embedding is that the Word or PowerPoint file is complete containing the Prism data and settings One disadvantage is that this makes the Word file larger Another disadvantage for some is that it means your data can be stored in multiple places If you realize the data was entered incorrectly you will need to edit all the copies Others see this as an advantage a way to backup your data A Prism object only includes the data tables and results that are linked to the graph or layout that you pasted Other parts of the Prism project are not included Paste a graph or layout as a picture A picture may be worth a thousand words but it doesn t let you edit data change analysis choices or reformat the graph When you double click ona pasted picture you cannot edit it within Prism Instead you ll open up a generic graphic or photo editor An advantage of this approach for some is that people you send the file to won t be able see your data or edit your graphs Bec
196. e an entire family of sheets with the new data analyzed and graphed From a data table not linked to any graphs or analyses click the Wand Wizard to ANalyze Data button Choose the table you want to use as an example and Prism will analyze and graph the current data exactly as it analyzed the example data Merge a graph and its family into a different project Copy the graph go to a layout of the other project and paste You ll get a choice of pasting just the picture a picture with a link to the first project or to merge in that family of sheets into the project that contains the layout The details of how a family is defined A family is the sheet you are looking at and all sheets directly related to that sheet So if you are looking at a graph the family includes the data table s 1995 2014 GraphPad Software Inc s GraphPad Prism User Guide plotted on that graph any analyses included on that graph as curves or embedded results tables and any layout s that include that graph There are three possible ambiguities e A graph can contain data from two more more data tables If you start from the graph and save or duplicate its family both all those tables are part of the family If you start from only one of those tables the other table s are not part of the family e Info sheets can either be declared to be linked to a particular data table or to be global to the entire project Prism includes an in
197. e border thickness and color and the background Or double click on the border of the text object to bring up the Format Text dialog Then click the Border and Fill button to bring up a dialog where you can change border and background To move text Move a text object by dragging You can also stretch the object to change its shape This will change how text wraps but will not change the point size of the lettering You can only move axis and graph titles closer to or further from the graph They always remain centered To move a title closer to or further from the graph point the mouse near the title until the cursor changes to a two headed arrow Then drag the title You can also move axis numbering or labeling for bar or category graphs closer to or further from the axis Click on the numbering to select Then use the arrow keys to nudge its position Or set the distance between numbers and axis within the Format Axis dialog To prevent text from snapping into alignment When you drag a text object around the page it will automatically snap into 1995 2014 GraphPad Software Inc GraphPad Prism User Guide alignment with other text objects with the center of bars etc on graphs or with the center of a graph You can keep dragging so are not trapped by the snapping If the snapping gets in the way of moving the text object where you want it hold down the ALT key while dragging and there will be no snapping 20 2
198. e ee If you choose to arrange the data By rows or by columns Prism reads the values row by row from your source file but ignores all line breaks It treats the data T as though it came from one column or one row 1 12 8 5 Info amp Notes tab Prism s Info Sheets are a place to store details about a project or experiment If you are importing data from a text file or pasting you can import ranges of information from a text file directly into a linked Info sheet in your Prism file 1995 2014 GraphPad Software Inc 180 GraphPad Prism User Guide f pas Import and Paste Special Choices i Source View Fiter Placement Into amp Notes Info constants into sheet Import into Note that lt info gt and lt Notes gt sections must come before any data Use these settings as the defauk for Import and Paste Special Restore orginal default Help Cancel Paste You can import this information at the same time you import your data Use the Info and Notes tab of the Import and Paste dialog to specify the rows you want to import and which Info sheet you want them to flow into If you can control the format of your text file you can include info constants and notes in structured sections at the beginning of the text file Mark the sections in the text file with lt gt variable names as below e Mark any values that you want to import to Info Sheets for
199. e fact that they are excluded 2 Followed by an asterisk 3 As a blank space instead of the value When exporting this choice is set in the export dialog When copying to the clipboard the choice is set in the File amp Printer tab of Preferences 1995 2014 GraphPad Software Inc z GraphPad Prism User Guide Choose whether to use period or comma as the decimal separator When you copy data to the clipboard Prism 5 used the Windows or Mac control panel settings to decide whether to use a comma or period point as the decimal separator Prism 6 lets you choose in the Preferences dialog This lets scientists who live in countries where a comma is commonly used still use a period when copying data out of Prism for pasting into a manuscript that will be read in other countries LinkBack support When you paste a graph or layout created with Prism 6 Mac into some other programs LinkBack let s you double click on the embedded graph to return to Prism for editing This works similarly to OLE on Windows But while OLE is part of Windows and supported by Microsoft LinkBack is not part of OS X and is not supported by Apple It only works with selected Mac apps and does not work with Word PowerPoint or Keynote 2 8 What s new Parts of whole data Parts of whole tables Prism has always created structured data tables and Prism 6 adds a sixth kind of table Parts of Whole As the name suggests this table is used for the kind of data wher
200. e it makes sense to sum all the values in a data set column and divide each value in the table into this total Pie charts and more Each data set column in the parts of whole table can become its own pie chart and each value represents one slice of the pie Prism will graph column A automatically To graph the other columns use New Graph of existing data Prism can also plot these kind of data as a donut plot stacked bar plot or a percentage dot plot 1995 2014 GraphPad Software Inc What s new in Prism 6 m A mA m e E B _c mc MD E o Totak 61 A 0000000000 m 0000000000 m mis 0000000000 m mc LOLI KLALI m o 0000000000 MD O000000000 oOo00000000 O000000000 0000000000 ee ecooooono Total 61 e A new fraction of total analysis computes each value in a table as a fraction or percent of its column total In a parts of whole table each value represents one Slice in a pie chart defined by the sum of all the values in that column so this analysis computes the fraction or percentage of the pie represented by each slice It can also be used with contingency or Column XY or Grouped if needed and if there are no subcolumns tables to compute each value as a fraction of its column total its row total or the grand total e Compare an observed categorical distribution with an expected distribution using either the chi square test any number of categories or the binomial test works only with two categori
201. e of Prism s strengths is its ability to handle replicates and error bars For XY and Grouped tables replicates are placed in side by side subcolumns For Column tables replicates are stacked in each column If you enter replicate values Prism can plot either individual replicates or error bars It can plot error bars from the replicates you entered automatically You don t have to specify any calculations When you edit or replace data analyses and graphs are automatically updated Prism remembers the logical links between data tables info sheets results tables graphs and layouts When you edit or replace data Prism automatically recomputes linked analyses and redraws linked graphs Analyses can be chained Results tables can be analyzed further Just click the Analyze button This lets you say first transform your data and then fit a curve nonlinear regression to the results One table one graph By default Prism creates one graph for each data table you create but this should not limit you You can plot a table on multiple graphs And you can plot data from multiple data tables on one graph Recycle your work Once you ve analyzed and graphed one data table it is easy to repeat your work with new data by duplicating a family or cloning a graph 1995 2014 GraphPad Software Inc Getting started with GraphPad Prism 53 4 3 Welcome dialog Welcome to GraphPad Prism When you launch Prism or use File New to
202. e secure for long term backing up Even without access to Prism the data in the file are in plain text that can readily be viewed The PZFX format is very useful for data interchange With a bit of work someone could write a program to replace the data in a PZFX file with new data When you open that file you ll see the new data analyzed and graphed Files saved in PZFX format tend to be much smaller about 10 the size than the same file saved as PZF We recommend that you use PZFX files routinely Don t use the PZFX format if you plan to send the file to someone using Prism 4 or earlier Prism 5 is the first version that understand the PZFX format Also don t use the PZFX format if you plan to post the file on a web site Web browsers sometimes detect the XML format and try to open the file with some program that understands XML rather than opening with Prism In contrast PZF files generally just open in Prism as they should XML format This format is virtually the same as PZFX but it also contains a XML style sheet which lets you view the file in any web browser You ll see nicely formatted data tables and info tables Compact format Prism has an option to save PZF files in compact format All the compact format does is leave out analysis results Files with lots of complicated 1995 2014 GraphPad Software Inc 12 GraphPad Prism User Guide analyses will be smaller if saved in compact form but all those analyse
203. e table name is a subset of the results and graph sheet names these will be substituted Suppose that the data table is October data and is linked to Nonlin fit of October data and Graph of October data If you start from the data table and choose to duplicate family you can enter November data as the name of the new data table Prism will then rename the linked sheets to Nonlin fit of November data and Graph of November data It can only do this because the exact name of the data table is part of the sheet names If you are starting from another kind of sheet Prism will ask you to enter a prefix that will be prepended to the names of all the duplicated sheets In the example above you could choose to preface all the newly created sheets with x These new sheets will be October data Nonlin fit of October data and Graph of October data Of course you can rename the sheet titles however you want Prism will duplicate the current sheet and all linked sheets Replace the data on the new data table and all analyses and graphs will update Note the distinction between duplicating a sheet and duplicating a family of sheets When you duplicate a sheet only that one sheet is duplicated If you duplicate a data table it will not be linked to any graphs If you duplicate a graph the copy will link to the same data table as the original This is useful if you want to make two graphs of the same data But if you want to make t
204. e the color or thickness of a scale bar Double click the scale bar to bring up the Format Object dialog Choose color and thickness in this dialog To remove the caps on the end of the scale bar By default the scale bars are capped These are actually arrowhead styles To change double click the scale bar to bring up the Format Object dialog Then change the arrowhead settings 1995 2014 GraphPad Software Inc Graphs Frame and axes 289 To move a scale bar Drag with the mouse Or click to select and then nudge by clicking the arrow keys To label a scale bar Scale bars don t include any numbering To create a label for a scale bar click the text tool T button click near the scale bar and type To change the length of the scale bar You can t change the length of a scale bar by stretching it Instead bring up the Format Axes dialog and change the tick interval in the Regularly Spaced Ticks section 15 2 6 Discontinuous axes Creating a gap in an axis When plotting scientific data you will often want to create a discontinuous axis and axis with one or two gaps Double click on the axis to open the Format Axes dialog In the Gaps and Directions section you can choose either a two segment one gap or three segment two gaps axis Format Axes Frame and Origin X axis Lent Y axis Right Y axis Titles amp Fonts No left Y axis Standard Range Reverse Automatically deter Minim
205. e to contain the text the script will output If you don t precede the file with disk and directory Prism will use the path defined in SetPath If there is no SetPath command then Prism assumes that you want to use the directory that contains the script If you include a delimiter say it will appear between entries Otherwise the output file will be delimited with tabs If the output file already exists Prism appends to that file unless you have included CLEAR Results will be tab delimited unless you include an alternative delimiter in the OpenOutput statement Examples OpenOutput C gp25 output txt Clear OpenOutput C data july97 You can write export data and results to the text file using any of the commands that begin with W or by creating a text or CSV table as described in the next section If you end any of the W commands with a semicolon the next W command will add text to the same line following a tab If you end with an ampersand amp the next W command will add text to the same line without a tab If you omit the semicolon or ampersand Prism inserts the codes for carriage return and line feed so the next W command will write to the next line in the file The most useful W command is WCell which writes out the contents of one cellina data or results table You need to specify the row and column of the cell to write Row O refers to the row of column titles and row 1 is the first row of data Col
206. e used for new graphs Pull down the Edit menu the Prism menu in Mac OS X and choose Preferences then go to the New Graphs tab 1995 2014 GraphPad Software Inc so GraphPad Prism User Guide 15 2 9 Dates Prism does not understand the concept of dates or times so you cannot enter times or dates as X values But you can get Prism to plot dates or times as row titles Note that Prism does not try to interpret the meaning of row titles To Prism you just entered labels The data will always appear equally spaced on the graph even if the dates are not equally spaced chronologically Most of the time your dates will be equally spaced so this approach works well But sometimes your dates are not equally spaced on the calendar and the graph is misleading Jani Feb1 Aprili Dec1 You ll need to use a different approach to plot a series of dates that are not equally spaced Enter the data onto an XY table Enter the dates as row titles Into the X column enter the number of days since some starting point 1995 2014 GraphPad Software Inc Graphs Frame and axes 301 8 Table format X Group A 6 a ef x Y 4 0 1 n 2 0 4 0 NON SS F To make this graph you ll need to make some changes on the Format Axis dialog Leave the Number Format set to Decimal Don t choose Row Titles or you ll end up with an equally spaced graph Use the Additional Ticks se
207. ease different columns 1995 2014 GraphPad Software Inc ns GraphPad Prism User Guide Analyses performed from a contingency table e Fisher s exact test e Chi square test e Odds ratios and relative risk Example of a contingency table Outcome Outcome B Outcome C Oi Table format ngency Success Failure Y Y Y 1 23 5 2 Treated 61 21 3 Treated with antagonist 21 43 4 5 The three rows represent three different treatments The two columns represent two alternative outcomes Each value is the actual number of subjects in this case in other cases the values may represent number of objects or events It is essential that you enter the actual number of subjects objects events that you counted Do not enter normalized values or percentages Since the values are counts they cannot be negative and must be integers Prism won t let you enter a minus sign or decimal point or create subcolumns If you need to enter fractions or negative numbers or create a table with subcolumns use a Grouped table instead 9 7 Survival tables On a survival table you enter information for each subject Prism then computes percent survival at each time and plots a Kaplan Meier survival plot and also compares survival with the log rank and Gehan Wilcoxon tests Analyses performed with survival data e Kaplan Meier e Log rank e Wilcoxon Gehan Example of a survival table 1995 2014 GraphPad Software I
208. ece ee ence ee eee nena ee eeae sees eeaaeeeeeeeeeeeeeeaeeeeeeees 76 8 Tips for working in a small WiIMGOW cccceteeee eens eeee ee ee ee ee eres eens eeeeaaeeeeeeaaeeeeesaaeeeeesaaeeeeeees 77 Part VI Organizing Prism projects 78 1 Renaming sorting and deleting Sheets ccccecceeeeeseeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeneneenens 80 2 Working with multiple sheets at ONCE ceccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeeeseeeeeeeeseneeneanes 81 3 Freezing a sheet to prevent ChANGES ccceeccseeeeeeeeeceneeeeeeeseeneeeeeeeeeneecenseneeeessaneeeeeessenee 84 4 Using Info sheets to organize your Projects cccecececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeneneees 84 5 Annotating your work with floating ANd audio NOTES ceccceeeeeeeeeeeeeeeeeeeeeeeeeeaeeeeeneeeeeeeees 87 6 Highlighting sheets in the Navigator tree ccccceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeeeeseeseneeenenes 88 T Preference saz ireciete teed ie a este Ne aa sa bece need eden AAAS chen eth Aaa A iteceosk cease A A AARAA 89 Part VII Work efficiently Repeat analyses and graphing 92 1 Duplicate a family of she ets oc cccticcsccctccceccctvesteeetvednettiestenetivecenettieenenetvestnetteesneeetveseretteanee 93 2 Clone a QraPhhececicccsesccicceevevecceeseerescevevecseevecttdceeeiessedeeevedecvevececeeeencceveeetecaveevetaasevetea stented ans 94 3 Repeat analyses with the Wand ccceseceeeeeeeeeeeeeeeeeeeeeeeee
209. ed and let you change font color and size Select a block of text or an entire text object and use the right click menu Or pull down the Change menu and choose Selected Text to bring up the font dialog Text 14 v Arnal v AAaABZU ui Wi A r 1995 2014 GraphPad Software Inc Adding text drawings and pictures to graphs or layouts 373 GraphPad does not provide any fonts with Prism but lets you choose any TrueType font already installed in your system If you want a font that is not in the list you ll need to find or buy the TrueType font and then install it into Windows or Mac OS X To rotate text You can rotate text objects to any angle you want Click on one of the text rotation buttons in the Text section of the Prism toolbar The buttons will rotate your text in 15 degree increments Text 14 v Arial v A AAB IU GE Or double click on the object boundary to bring up the Format Text dialog Then set a standard rotation horizontal vertical up vertical down or choose angled and enter the rotation angle in degrees To change the alignment of a text block Text 14 v Arial AABZU ui S Click on the Justify button on the Font toolbar From the drop down menu you can choose right justified left justified or centered Whichever you choose will be the default the next time you enter text To add or change a border or background Right click on a text block and you ll see choices to change th
210. ee on the Prism screen which internally uses RGB Many scientific journals now request RGB Select CMYK only when submitting images to a journal that insists on CMYK Learn more about the differences between RGB and CMYK here and here Fonts and EPS files Prism Windows but not Mac offers two choices about how to handle fonts when exporting to EPS format The default choice is to choice saves the text into the EPS file as characters with references to the fonts you used If you have used only standard fonts this format lets others edit the text and change the font and size The only drawback is that if the file is opened on a computer that does not have the exact fonts you used another font will be used and the appearance can change drastically A font that looks like this may care out looking like this Prism Windows also offers an option to convert all text to outlines so that each letter is described as a set of graphic objects without reference to any font file Prism Mac always exports EPS in this format The advantage of this approach is that the look of your graph or layout will be preserved on any computer even one that does not have the fonts you used The disadvantage is that the text no 1995 2014 GraphPad Software Inc Exporting images from Prism 393 longer is encoded as text That means it is impossible to opens the eps file and edit the text change the point size or switch to a different font A
211. eeeeeeeeeaeeeeeeeeeeeeeseaeeeeeseaneenees 115 5 Grouped tables two grouping Variables cccececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeesenees 116 6 Contingency table Siccicscssccce csfeccecac vende cc ecens aee a enaa REDA Po veers ccyacved Enar AERES TARA Da ESNA S POENE 117 7 Survival table Sis cskern innuna annn kna aaa ANANA cc NAERA a AARNE sates AA ANADA kA AREAREN n ANANE AANA RS 118 1995 2014 GraphPad Software Inc 4 GraphPad Prism User Guide 8 Part X O AN Oo FP WN a 2 2 2 a fF WwW N a O amp O Part XI O AN Oo FP WYN Part XII oN OO a FF WD Parts of whole tables c ccccccsssseeeesseeeseeeens Data tables How to create a new data table Data table limits c ccececeeeeeeeeeeeeeeeeeeeeeeeees Changing a data table format c0e Choosing a table to create a bar graph Choosing a table to create a scatter plot Column title Siiiicsscccseccceesesstentas annann Row title Sis csctccic stacks netiviiiesiarasenneteicetennet ecient Sorting data ccccceeeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees Changing data table column widths Specifying decimal placesin a data table Excluding data table values from graphs and analyses Missing ValUCS cccceeeeceeeeeeeeeeeceeeeeeeeeeeeneeees Keyboard Shortcuts ccccceeeeeeeeeeeeeeeeeeeeenees Inserting a SCTIOS ce ceeceeeeeeeeeeeceeneeeeeeeeeeeees ROUNGING ieecccecc irera feel sete deecinecende
212. eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseneeneanes 96 4 Tem plate Si ehi aiaa a aaraa aa aa neta a eaaa a E aaa aaa aai aaa o Ea eaa ienaa aaa EAEE iia 97 5 Template or method wand ssssssssssesssnnnennnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnna 98 Part VIII Prism files 99 1 Saving file formats and comMpresSioOn ssssssssssssrnrnennnnnnrnnnnnnnnnnnnnnnnnnnnnnnnannnnnnnnnnnnn nnne 100 2 File compatibility between Prism versionS ssessesssnennnennnennnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnennnenn 102 3 Backing Up Prism fle Scinaia eaaa i a AAA aa ia aa EAEAN AAR EES OANE RE ADARA AANE i 103 4 Merging and splitting projectS sssssesssrnnnrnnnrnnnnnnnnnnnnnnnnnnnnnnnunnnunnnnnnnnnnnnnnnnnnnnnnnn nnmnnn 105 5 Emailing Prism files to CONC AQUCS ccceeeeceee ee eeeeeeee ee eeeeee ee eeeeeeeeeeeeee ee eeeeeeeeeeeeeeeeeeeseneaes 106 G LabANChive ERNE ected cee sececutcze vey dee escatvet dc vssuheedeedseite ver cused E E T 107 Part IX Distinguishing the six kinds of data tables 108 1 Key concept data tables c ic o5 ifecsecceesccceceecdeeccnsccoseccedveccs cones cee sdeeceteceseqeeastecetidesede 109 2 Prism s six data table formats ii iccciiccoscccie csvevieecoverseecsveveeecavecse cb venience vecedeccveveieccuexseecaeeees 110 3 XY data ta De Sisri eea aoa a aa a aa Aa cowee sea sdecceesvacvencutsseiseccueecead 113 4 Column tables one grouping variable ccccsecccceeeeeeeeeeeeeee
213. een i You may need help from your webmaster FTP Options FTP host address Le ftp somewhere com or 192 168 37 1 FTP user name FTP password FTP folder Use passive PASV mode URL to view on the web Le http www somewhere com Prism Updates W Automatically check for new Prism versions Enter the ftp URL and your account name and password if required You must also enter the URL to use to view these files Prism will append the folder and file name If your server is behind a firewall that prevents incoming FTP connections check the option to use passive mode so Prism will initiate data connections rather than asking the server to connect back to your computer You may want to ask your webmaster for help in configuring these FTP settings 22 Printing 1995 2014 GraphPad Software Inc Printing This section explains how to print graphs and layouts and how to change your printing options 1995 2014 GraphPad Software Inc GraphPad Prism User Guide 22 1 Two toolbar buttons for printing The Print section of Prism s toolbar has two buttons for printing C l _ Print the current sheet or multiple sheets selected in the Gallery using your default Print settings fmi Bring up the Print dialog to choose a printer and which pages to print 22 2 Printing data and results tables Choose font size Change the font size to control the size of the print on the page and thus
214. emplate A template is a Prism file that you recycle Choose a template add new data and all the analyses and graphs will be created automatically Templates are an older feature and we recommend you clone a graph or use the Wand instead A Prism template is a regular Prism file with three differences e A template has the extension pzt When Prism opens such a file it will forget the file name and open the file without a name Then it will prompt for a file name when you save This prevents accidentally overwriting the template e When you save a template you can enter some brief instructions that will appear when the template is opened This can be useful when you are creating a template for others to use e A list of templates will appear on the Open a File tab of the Welcome dialog Creating a template 1995 2014 GraphPad Software Inc 98 GraphPad Prism User Guide Follow these steps to create a template 1 Create a Prism project with only the sheets you want to see when a template is opened 2 Optional Delete the portions of the data that will change with each experiment for example delete the Y values but leave the X values and the column titles Don t delete entire columns just the values in those columns by selecting and then using the Delete key 3 Go to the data table you want to see when the template is opened drop the File menu choose Save Special and finally choose Save Template You ll al
215. en data points overlap You can fine tune that order in the Format Graph dialog The two graphs in this example are identical except that the plotting order was reversed Signal On Column Grouped and Contingency graphs this reverses the left to right order You can also fine tune that order Flip between portrait and landscape orientation You choice of portrait or landscape only matters when you print the graph from the Graphs section This choice does not change the aspect ratio of the graph Rotate entire graphs Rotate between vertical and horizontal presentation of Column Grouped and Contingency graphs Treated Antagonist Treated Control 100 150 Signal gt 1995 2014 GraphPad Software Inc Prism Graphs the basics 205 13 11 Formatting individual symbols and bars Change the look of a single point or column Right mouse click on the point and choose Format this Point You can change the symbol shape size color and the format color and direction of the error bars Effect of Neural Stimulation on Blood Pressure o ee toe AZ Symbol Color F bre Dota Set Symbol Shape gt Format All Data Sets gt Symbol Size gt Systolic blood pressure Remove Data Set from Graph Replace Data Set Keep Only This Data Set Reverse Data Set Order Control Stimai Send Data Set Back Bring Data Set Forward Error Bars Color Plot Deta Set On Error Bars Style 2 Stimulus
216. en you enter information on the Filter tab about which rows to include start counting with the first row following the structured information 12 9 Troubleshooting Negative numbers become positive fractional numbers become integers Situations where negative values become positive when pasted or imported into a Prism table e In a contingency table the rows denote treatment or exposure and the columns denote alternative outcomes Each value is the actual number of subjects objects or events Thus all values must be positive integers or zero If the data you are importing has any negative values the minus signs are simply ignored so the value will become positive If you want to include negative numbers you are not really creating a contingency table Drop the Change menu choose Format Data Table and choose a different kind of 1995 2014 GraphPad Software Inc 182 GraphPad Prism User Guide table You probably want a Grouped table e Excel can be configure to show negative values in red without the negative sign When you copy and paste this to Prism the color is lost but the negative sign is not restored e Some financial programs show negative numbers within parentheses Prism does not understand this syntax and the numbers will not be pasted as negative values e In a Survival table the Y values are a code One value usually 1 indicates that the event often death occurred The other value usually 0 indicate
217. ent colors Select one axis drop the Change menu choose Selected Object s and set the color and thickness on the Format Object dialog that appears To create a graph with three Y axes Prism does not allow three Y axes You can however create that effect with a bit of a workaround Create a graph with no data Hide the X axis one of the choices for axis frame Delete all the titles You are left with just a Y axis You can make that whatever scale makes sense Now make a layout and put your real graph next to this bogus graph with only a Y axis With some fussing to get the sizes to match and the data scaled right you can give the illusion you want You ll need to tell Prism to plot all the data sets on either the right or left axis SO may need to transform your values to make this work well Limitations Prism always draws the right X axis if there is one the same length as the left axis and starting and stopping at the same position on the page If you want one of the axes to be shorter the only way to get that effect is to cover up part of one of the axes with a drawn rectangle that you then make white or whatever your page background color is 15 2 5 Hide an axis and show scale bars Hiding the X or Y axis Or both Prism lets you hide either the X or the Y axis and show scale bars instead 1995 2014 GraphPad Software Inc Graphs Frame and axes 287 smv To hide and axis and show a scale bar instead Do
218. ently used files user defined equations color schemes and more You can use a startup option to tell Prism to not save any changes to the preferences file This is useful in a teaching lab or a shared computer so Prism will always start with the same preferences C Program Files GraphPad Prism 6 prism exe C 25 3 Technical support Check for program updates Like all software companies GraphPad occasionally issues minor updates to Prism The full version number is not on the CD Instead drop the Help menu and choose Check for updates Check for answers on graphpad com If you can t find the answers in these help screens please visit our support web site We update the Quick Answers database almost every week and the answer to your question is very likely to be there Personal support Drop the Help menu and choose Personal support command Prism will instruct your email program to create a new email automatically including your version and serial number and attaching if you choose the file you are working on 1995 2014 GraphPad Software Inc so GraphPad Prism User Guide If the Personal support command does not work on your computer or you use a Mac email us at Ssupport graphpad com Be sure to mention the version of Prism you are running and if you are using Prism for Windows or for Mac To find the version number drop the Help menu Windows or Prism menu Mac OS X and choose About Prism Wind
219. ers three choices Excluded values can appear e Just like all other values ignoring the fact that they are excluded 1995 2014 GraphPad Software Inc Importing and exporting data 189 e Followed by an asterisk e As missing values blanks What should the decimal separator be You have three choices e A period or point 1 23 e Acomma 1 23 e Let Prism decide based on your Windows or Mac control panel These choices are set in the export dialog when you export to a file When you copy the data to paste somewhere these choices are set in the File amp Printer tab of Preferences dialog 1995 2014 GraphPad Software Inc 190 GraphPad Prism User Guide 13 Prism Graphs the basics A picture is worth a thousand words Prism makes it easy to create the graphs you want Choose a type of graph enter your data and Prism automatically creates a graph Because graphs and data are linked if your data changes 1995 2014 GraphPad Software Inc Prism Graphs the basics 191 your graph will automatically be updated Once you ve made your graph you can customize any part of it This section contains the key things you need to know to get started with graphs 1995 2014 GraphPad Software Inc 192 GraphPad Prism User Guide 13 1 Creating graphs Creating a new data table which will be automatically graphed When you create a new data table Prism automatically creates a linked graph C
220. erval or range 8810 Fit a family of curves at once E Global shared A B Treated Place data for multiple data B Nonlin fit sets side by side on an organized data table and fit them all at once You can fit Ses l ales the same model separately to each data set use global nonlinear regression to share parameter values among data sets or fit different models to different data sets Control One phase decay Plateau K Half Life Tau Span Easily handle missing and excluded values Using a command on the View StouPA Group B menu or via right clicking ora toolbar button exclude selected values Excluded values show on the data table in blue italics but are omitted from analyses and graphs You can also leave a cell blank to show that its value is missing Prism treats missing and excluded values identically and never treats a missing or excluded value as if you entered zero Computed values are kept separate from raw data 1995 2014 GraphPad Software Inc 4 GraphPad Prism User Guide 3 2 Prism includes built in analyses A B Treated Control to transform or normalize your 4 A Y1 A Y2 A Y3 B Y1 B Y2 B Y3 data or to subtract or divide 3 949 3 867 3 983 3 815 3 898 by a baseline Prism leaves yo
221. ery Sheet Ox bie Je New Use floating notes to communicate with coworkers Click the push pin icon to add a color coded floating note to any sheet Sheet 2B XY Floating note XKX 3New 1995 2014 GraphPad Software Inc 3 Bj GraphPad Prism User Guide a Record experimental details on info sheets Info sheetscontain both structured information lot numbers page numbers and unstructured notes Each info sheet can be linked to a particular data table Don t make projects too small or too large Some people make the mistake of starting a new project for every data table not realizing that a Prism project file can have up to 500 data tables analyses and graphs You can keep an entire project in one file Don t define project too broadly because a huge project can be hard to navigate You can always merge projects later or include a graph from one project in a layout of another Common mistakes Mistake Repeating an analysis rather than fixing it If you want to change your mind about analysis choices you can do so You can change the parameters options for the analysis Or you can change which data table and which data sets are analyzed There is no need to start the analysis again which leaves an obsolete copy of the results in your project Mistake Duplicating a table in order to make a second graph of those values Prism automatically makes a graph of each data table
222. es 1995 2014 GraphPad Software Inc z GraphPad Prism User Guide 2 9 What s new Column graphs Superimpose individual data points with bars 200 150 100 50 Control 1 Hour 6 Hours 24 Hours Superimpose individual points on a box and whiskers plot 200 150 100 50 Control 1 Hour 6 Hours 24 Hours Separate groups of columns with a line 1995 2014 GraphPad Software Inc What s new in Prism 6 200 150 100 50 Control the length of the mean or median line in a scatter plot Short Medium Long Connect column means with lines 1995 2014 GraphPad Software Inc s GraphPad Prism User Guide 200 150 100 50 0 Control 1 Hour 6 Hours 24 Hours 2 10 What s new XY Graphs e Depth charts When you assign a graph to a layout you can specify that it be rotated 90 degrees This essentially creates an XY graph where the independent X variable is shown on the vertical axis As the graph s name suggests this kind of graph is used in fields where the independent variable is depth which is naturally shown on the vertical axis 1995 2014 GraphPad Software Inc What s new in Prism 6 31 po 0 50 100 150 0 Heo y 2 Heo g 2 eH 4 ond a em 6 eH e Label both sides of the axis Place additional ticks and labels across the axis from the regular numbering This is helpful for example when X is time but you also want to label particular times when a
223. es included in this list Let us know if there are parameters missing and we can add them in a future version Hits tab optional If you skip this Hits tab Prism will tabulate the selected parameters different columns for each simulation rows Prism can also reduce the results down to a single number the fraction of the simulations that are hits Define a hit to be when a value tabulated by the analysis equals a certain value or is within a specified range Click New Graph of existing data from this table and choose a parts of whole graph to create a pie graph of the fraction of hits vs not hits Prism can also tabulate the selected parameters only for simulations that are hits and or for only the simulations that are not hits Choose any or all of these options Hits Not hits All simulations at the bottom of the Hits tab Each option you check will create its own results table 1995 2014 GraphPad Software Inc Simulating data and Monte Carlo simulations 339 17 3 Monte Carlo example Accuracy of confidence intervals Overview When you fit a curve with nonlinear regression one of the most important set of results are the 95 confidence intervals of the parameters These intervals are computed from the standard errors which are based on some mathematical simplifications They are called asymptotic or approximate standard errors They are calculated assuming that the equation is linear but are applied to non
224. es of freedom Prism generates df 1 different random numbers drawn from a Gaussian distribution Random numbers from a Poisson or Binomial distribution We adapted ideas from pages 372 377 of Numerical Recipes third edition by WH Press and colleagues Random numbers with Excel If you want to do simulations not possible with Prism it might be possible with Excel The methods listed below work well with Excel 2003 and later but should not be used with earlier versions of Excel Excel offers two random number functions e The RANDBETWEEN low high formula chooses a random integer randomly from the range between and including the low and high values entered The result is always an integer so this function is not very useful e The RAND function generates a random value between 0 0 and 1 0 It is an Excel function at least in name so it needs to be followed by parentheses but the function has no inputs so there is nothing between the parentheses If you want to generate random numbers from a Gaussian distribution you ll need to transform the values generated with the RAND function This Excel formula computes a random number from a Gaussian distribution with a mean 1995 2014 GraphPad Software Inc Simulating data and Monte Carlo simulations 345 of 0 0 and a SD of 1 0 NORMSINV RAND The RAND function calculates a random number from 0 to 1 the NORMSINV function takes a fraction between 0 and 1 and tell
225. esaeeenaeeesaseesaeeeeaeeseaeeesaeeeneaeessaeeeseeeensaeeesaees 271 Customizing a graph s frame and axes appearance ccceeceeeeeeeeeeceeseeeeseeeeeeneeesaeeeseeeseeeeesaeeesaeeeeeeeeees 273 Showing grid LIMES eeeseeeeeeeeeeeeeeeceeeeeeeeeeeeeeaeeeeeneeeeeeeeseeeees Setting the graph origin AXIS SANGO sciccestscuciccssevceavessccivesevseueesaenensvecessesusssuesuscecvanceisousluscsceseavexsucisssesteueesdeueassuestsesuescessscerseatennenel sstbersuevers Axis numbering or titles Major and minor ticks Graphs with a right Y axis Hide an axis and show scale bars DIS CONTINUOUS AXE Sj cesivvisscensecevecevesencescsccvesscesseceasncevendecesneensivchlcteesesreustuevecvasssniesssecactseduevenstvesendevesavenceressersustars Additional ticks and grids Axis titles scccsscvsescivssscrssersecaveress Dates E E E E A a E E E T A E A A garithMic aXe S a a a a anA Aa a E a EE A EEA dEn What is a logarithmic axis Pssst aaea aeaa Aer Eea ae ea A aa A A daia rea 302 How to Create a log axis Logarithmic axes cannot contain zero or negative numbers Regression fits the data not the Graph c ccceseeeseeeeeeeeeesneeeeeeeneneeeeaeeeeaneensneeseaneesaeeenaeeesaeeeseeeenseeeesaees When to use a logarithmic axis sssini araida dik renards rea eaa ea EASi aaa taidat Advice Bar graphs with log axes rarely make sense Graphing logarithms different than using a log axis r AAA OE A E A EE A T E E E E
226. eseeeeeeeseneees 462 Gs PANNING see co ae ae aces cate cen nee Sueate veh cee bs pacas T so vex cua sd tenvad copecdes dceaetebecrteestgreevetdarres 467 Index 469 1995 2014 GraphPad Software Inc 10 GraphPad Prism User Guide 1 How to learn Prism Browse the Statistics and Regression guides This Prism Guide is only one of three guides Check out the other two Both do more than explain how to use Prism They also explain the concepts of data analysis e GraphPad Statistics Guide e GraphPad Curve Fitting Guide Step by step tours Read this one page tour which will take about five minutes to follow Then follow longer detailed tours that walk you step by step through data analyses and graphing Work with sample data sets Choose these from the Welcome dialog Each sample data set comes with brief instructions and links to longer explanations Ne Y Welcome to GraphPad Prism S Column tables have one grouping variable with each group defined by a column A B Ej Control Treated 1 2 om Control Treated Learn more Enter import data Enter replicate values stacked into columns Grouped Enter paired or repeated measures data each subject on a separate row P Enter and plot error values already calculated elsewhere Contingency Use sample data Frequency distribution data and histogram t test Unpaired ttest Paired ttest One sample Sur
227. exports to the JPG format with the least possible compression making larger files but sharper images Any compression would reduce the clarity of your graphs noticeably PNG The PNG format is great for posting graphs on web sites PNG files use screen resolution which is fine for displaying on screen but is too little resolution for submission to printed journals There are no options of color depth or resolution BMP PCX PICT 1995 2014 GraphPad Software Inc Exporting images from Prism 389 These formats are older especially pcx formats that don t offer any advantages Choose only if your publisher or another program needs one of these formats Note that Prism 6 Mac exports PICT files as bitmaps with no font or vector information 21 4 Exporting for publishing in journals When you submit figures to journals for publication you have to decide which format to use Each journal has their own rules and these sometimes change But here are some general notes on preparing Prism graphs for publication Exporting as a TIFF file Exporting as TIFF our customers tell us usually works well Notes e In most cases you will want the page background in Prism to be white and to check the option in the Export dialog to include that color in the file Transparent backgrounds can sometimes cause problems e For resolution try to follow your journal guidelines It would seem to make sense to choose the highest resolution
228. ext file directly into a Prism Info sheet 1995 2014 GraphPad Software Inc GraphPad Prism User Guide 12 8 1 Source tab la Import and Paste Special Choices h ne Source View Fiter Placement Info amp Notes Fie Paired t test data AlAd Linking and embedding Insert data ory Insert and maintain link tically update table with Inke Excel Use these settings as the defauk foe Import and Paste Special ee TE Restore ongnal def aut Help Cancel Pase Linking and embedding Insert Data only Prism retains no link back to the Excel spreadsheet or text file The values will be pasted and nothing else The only advantage to using this method is that it is conceptually simpler Insert and Maintain Link Paste or Import the values into the data table but also create a link back to the original file The link has two functions It lets you trace and document the source of the data so you stay organized It also is a live link If you edit or replace the data in the original data file Prism will update the analyses and graphs With Prism for Windows you can link directly to a text or Excel file Prism for Mac will link only to text files With Prism Windows the Link option is available only if you paste from an Excel workbook that has a name If you are working with a new Excel file you must first save it thus giving it a name before you can link its data into Prism Embed as OLE object W
229. extensive selection of sample data sets Simply choose one follow the detailed instructions lemme Let Maes pe and you can analyze data and make a graph in minutes GraphPad Learn to use Prism Open a file Correlation or Spearman Area under curve Organization of data table Column Grouped Contingency Survival Opened project specific binding only Binding Compare two models Fh le sooo a i competitive antagonist Global nonlinear regression Recent project nter and olot ard Operational model of agonist action global nonlinear regression Ente and plot emc Maki an XY bar graph Conelation Saved example Shared example 1995 2014 GraphPad Software Inc What s new in Prism 6 35 GraphPad Prism March Progress Summary pzf Exp decay with outlier ES 4 File Edt View Insert Change Arrange Window Help n O 2 2 82 x xokk GMA gt v Veina vA B OpenPismtier BH X rim 09 OO Sanse By w A TOA AC BIUXX ar a amp Family Data with Results 1995 2014 GraphPad Software Inc EN GraphPad Prism User Guide Magic Step 2 Choose properties of example graph to apply 5 Example graph Original One way ANOVA data First look grouped data Properties to apply Graph origin and appearance Range and ticks of axis With changes Fonts used for numbering and titles V Additional ticks amp grid lines with labels First look grouped data Appeara
230. f error plotting 1995 2014 GraphPad Software Inc Error bars and replicates 153 11 5 Stacked vs side by side replicates Note that replicates are arranged differently on different kinds of data tables e With XY and Grouped tables replicates are entered into side by side subcolumns e With Column tablees replicates are stacked into columns e When entering data on Contingency Parts of whole or Survival tables you never enter replicate values so this distinction is irrelevant 11 6 Error bars and confidence bands on Survival graphs Survival tables offer no choices for data entry When you create a Survival table you have no choices for data entry You don t enter error values Instead Prism computes the SE or 95 CI of survival when it creates the survival curves from raw Survival data Learn more about entering survival data If you want to enter survival fractions with SE values computed elsewhere create an XY graph In this case Prism will not be able to compare survival curves Choosing how to plot error bars The Welcome dialog not only lets you choose the basic type of graph via thumbnails on buttons it also lets you choose how to plot error values At each time point choose to plot the standard error the 95 confidence interval or no error bar Error bars None SE 95 Cl Changing how error bars are plotted To plot the replicates or error bars differently you don t have to remake a graph In
231. ferential equations It is no fun to struggle with algebra and calculus to express a model as an equation that defines Y as a function of X and parameters It can even be impossible Instead express your model as a differential equation enter the equation that defines dY dX as or an implicit 1995 2014 GraphPad Software Inc z GraphPad Prism User Guide equation an equation where Y appears on both sides of the equals sign e Write more complex models Prism 5 let s you define different models for different data sets by designating certain lines in the equation to only apply to a certain data set For example a line in the equation preceded with lt B gt applies only to data set B Prism 6 extends this syntax to allow more complex equations Precede a line with lt A D gt for it to apply only to columns A D or with lt A K 2 gt to make it apply to every second data set between A and K A C E G I K e New weighting choice When fitting a model to data with nonlinear regression it is important to weight the data appropriately This choice is often ignored but it can affect the regression results Prism always offered several choices for weighting Prism 6 offers a new weighting choice weighting by 1 Y where K is a constant you enter on the weighting tab of the nonlinear regression dialog Additional results with nonlinear regression e Hougaard s skewness When you write a user defined equation to fit to data with
232. float as in the example below o Baseline Automatic Bars begn atY 20 F Hide baseline 70 60 50 40 E a 5 10 0 ec F F Dimensions Prism automatically adjusts the width of columns based on the size of the graph the number of data sets and the gap between bars which you set here To make the columns wider make the spacing smaller Space between columns 25 of column width osB8ss3se es 888883 Fe Discontinuous axis 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 237 When you have a gap ina Y axis choose whether or not you also want a gap in any columns that span the gap Discontinuous axis Jl When the axis is dscortinuous also make the bars or connecting lines discontinuous Reset any individual bar formatting If you have changed the format of individual bars by right clicking on them check an option here to reset everything back to the format set in the dialog 14 2 5 Box and whiskers graphs What values do the box boundaries line and whiskers represent The box The box always extends from the 25th to 75th percentiles These limits are sometimes called the hinges of the plot Surprisingly there are multiple ways to compute these percentile values Prism uses a standard method but a different method than Excel uses The line in the middle of the box is plotted at the median You can not choose a different value but Prism also lets
233. fo table when you first create a new project file and this info table belongs to the project and is not linked to the first data table To choose go to the table drop the Change menu and choose Link to data table If an info table is linked to a data table then it is part of any family that includes that table If the info table is not linked to a particular data table then it will not be part of any sheet s family with one exception The exception is that when the project contains only a single info table and all the other sheets in that project are linked to be part of a single family then that info table is defined to be part of that family too e Don t confuse two uses of the word family The term is also used when Prism does multiple comparisons after one or two way ANOVA The multiple comparisons calculations are done so the probability alpha applies to the entire family of comparisons This use of the word family in multiple comparisons has nothing to do with a family of sheets 4 6 Adding new sheets to your project Sheet ZR i x D Click the New button on the Sheet toolbar and choose what kind of sheet you want to create The first choice is used the most It adds a new empty data table and linked graph to your project You can also add a new Info sheet a new graph of an existing data table or a new layout To be complete this menu also lets you add a new analysis but you ll find it easier to start at a data table
234. g and then add random scatter More often you will choose an equation on this tab Parameter values tab On top of the tab choose how many data sets you wish to simulate and how many replicates each data set will have The main part of the tab is where you enter the values of each parameter If you choose to simulate more than one data set then you can choose to enter a parameter value just for one data set or to enter a parameter that applies to several or all curves Choose the data sets on the top part of the dialog and enter the parameter values for that data set or that group of data sets below Random error tab Choose among several methods for generating random scatter and also adding outliers 17 2 How to Monte Carlo analyses How to begin a Monte Carlo analysis 1 Simulate a data table using one of Prism s simulation analyses Note that these simulations include random scatter so will produce new results when they are updated 2 Analyze that simulated data set as appropriate 3 From that results page click Analyze and choose Monte Carlo analysis This analysis will repeat the simulations many times and tabulate selected results The Monte Carlo analysis will only be available for analyses that create analysis constants Note that linear regression does not but you can fit a straight line with the nonlinear regression analysis The explanations below explain the basic ideas of the Monte Carlo analysis Follow the exa
235. g enter or import data data and then look at and fine tune the results and graphs e Methods are different First create a data table and enter or import data Only then do you click the Wand button to apply the method to your data Perhaps this distinction will help A template is a noun a place you start from A method is a verb something you apply to data you have already entered 8 Prism files 1995 2014 GraphPad Software Inc 10 GraphPad Prism User Guide A Prism project file or PZF file contains all the pieces of a project 8 1 Saving file formats and compression Prism can save in three file formats 1995 2014 GraphPad Software Inc Prism files 101 When you Save a Prism file you save the entire project into one file You have a choice of three file formats PZF format This is a binary format that can be opened by Prism 4 5 or 6 but not by other applications These files are a bit larger when saved by Prism 6 than previous versions because Prism 6 saves some extra information to ensure downward compatibility PZFX format This is a format that can be opened only by Prism 5 or 6 and not by Prism 4 The first part of the file contains all the data tables and info sheets in a plain text XML format that can be viewed by other programs After that comes information about results graphs and layouts in a format that is incomprehensible to any program but Prism The PZFX format is a bit mor
236. g will minimize as will Prism while the script runs Editing a script 1 Click the Prism button or drop file menu and choose Run Script 2 Choose one of the scripts listed in the menu Or choose Open Script file to open a script in an external file 1995 2014 GraphPad Software Inc 3 Follow steps 4 through 7 above 23 3 2 Run a script using Automator MacScript or AppleScript Run a script using Automator If you use OSX 10 4 Tiger or later Prism installs an Automator Action that lets you launch a Prism script The inputs to this Action is either a file containing a Prism script or the text of the script itself The output is either the word Done or an error message Run a script from Microsoft Office using MacScript MacScript commands let you launch Prism from Word or Excel These examples assume you are running Visual Basic for Applications VBA from within Excel Launch Prism with this MacScript command MacScript tell application HD Prism4 Prism Chr 13 _ activate Chr 13 _ open file Macintosh HD Prism4 Scripts dr2 Chr 13 _ end tell The MacScript command has to specify both the full location of Prism and the script that Prism will launch The MacScript command is a Visual Basic statement that you will need to write in an Excel macro perhaps one that runs when the user clicks a button As soon as Visual Basic has launched Prism it will
237. gator shows you which sheets are linked to the current sheet Their names are bold If you have a large project you may have to scroll to see all the linked sheets Prism therefore lets you see them all at once Click the plus sign in front of the Family folder to see a list of all sheets linked to the current one Alternatively click on the word family itself to see all linked sheets displayed in a gallery 1995 2014 GraphPad Software Inc seer 2O info O Resuts O Graphs O Layouts GQ Floating Notes Or click the Link button in the bottom toolbar to jump to one of those linked sheets Working with families of sheets To save a family of sheets Drop the File menu and choose Save Special and then Save Family As Choose a location and file name and Prism saves just the current family of sheets into that file The current full file will remain open and Prism will open the new smaller file in a smaller Window Be careful not to mix these up To delete a family of sheets Click on the plus sign in front of the Family folder to open it While pointing at that folder right click control click for macs and choose Delete Entire Family from the shortcut menu To duplicate a family of sheets From any sheet click the New button on the toolbar and choose Duplicate Family Alternatively right click on any sheet in the navigator and choose Duplicate Family Starting from a new data table creat
238. gered J Show syiitor Color GE Shape a a Size 4 sf X 2 pt Chow hare Jenik as rinnlinas Column scatter graphs If you want to compare groups and show every data point along with lines for mean and error for each group start with a column table All the data values for each group should be entered in a single column 100 80 60 40 20 Male Female To make the graph above start with a Column table and enter all the data points for each data set in a column Prism will create error bars from all the data points in each column Group A Group B of Male Female 7 T 54 4 23 45 G 54 7 45 4 If you instead want a graph that shows only the mean and error for each data set double click on any data point to open the Format Graph dialog and 1995 2014 GraphPad Software Inc 130 GraphPad Prism User Guide choose One symbol per column and the type of error you want to show Formal Grant O 3 E p Appearance Data Sets on Giaph Graph Settings Data set Data 2Male zj lt fi CD Style lt gt lt Bars Fil ae Pattern Patten color v Border Border color aE Symbols Grouped scatter graphs If you want to create a scatter plot comparing groups by more than one variable enter data on a Grouped data table with side by side replicates Table format Group A Group B Wild type cells WTC91 cell line d x A Y2 A Y3 A Y4 A Y5 BY1 B Y2 B Y3 B Y4 B Y5 1 Serum starve
239. ges New graph J Create a new graph of the results To normalize between 0 and 100 you must define these baselines Define zero as the smallest value in each data set the value in the first row in each data set or to a value you enter Define one hundred as the largest value in each data set the value in the last row in each data set a value you enter or the sum of all values in the column Prism can express the results as fractions Or percentages Notes e If you have entered replicate values zero and one hundred percent are defined by the mean of the replicates It is not possible to normalize each sub column separately e The X values are copied to the results table They are not normalized e Each SD or SEM is normalized appropriately e If you normalize to the smallest and largest value in the data set you can remove those values which would become 0 000 and 1 000 from the results 1995 2014 GraphPad Software Inc Transforming normalizing etc 355 18 5 Transpose rows and columns Each row of Y values becomes one column data set in the results table The first row becomes the first data set the second row becomes the second data set etc You may not transpose a data table with more than 104 rows because Prism cannot create a table with more than 104 columns The column and row titles in the results table are determined by your choices in the dialog Don t forget to check the option box if you
240. ging two Prism projects To merge an entire Prism project into another drop the File menu and choose Merge Pick a file which must not be open and all sheets from that file will be appended to your current project Prism places an asterisk in front of the name of each merged sheet It is also possible to merge just one graph and its related sheets into another Prism project To do this do not use the Merge command Instead copy a graph from one Prism project and then paste it into a Layout in another project The Place Graph on Layout dialog lets you choose to merge the graph and data into the new file The alternatives are to maintain a link to the original Prism file so that changes in the original will update in the current file or to paste just a picture of the graph Splitting Prism offers two approaches to splitting apart a Prism project To save one family of sheets into a new file choose Save Special from the File section of the Prism toolbar and then Save Family As This will save the current sheet along with all linked sheets To save the entire project with a new name drop the File menu and choose 1995 2014 GraphPad Software Inc 106 GraphPad Prism User Guide Save As Once you ve saved a copy of the file or part of it you ll want to delete unwanted sheets from the original project The easiest way to delete several sheets is to go to the Gallery for a section and click the checkbox on several sheets
241. graphs themselves remain they just have fewer or no data plotted on them Any results sheets based on the deleted data become orphaned you can still view and graph orphaned results but can t change the calculation parameters When you delete a graph sheet you also delete that graph from all page layouts but you will not delete the page layout sheets themselves 6 2 Working with multiple sheets at once View all sheets in the gallery Click a section title in the Navigator Data tables Info sheets Results Graphs or Layouts to view thumbnails of all the sheets in that section We call this the Gallery Use the Zoom buttons on the bottom toolbar to make the Gallery thumbnails larger or smaller QQ 1995 2014 GraphPad Software Inc 82 GraphPad Prism User Guide The gallery is useful for navigation and organization Double click on any sheet to go to it Drag and drop thumbnails in the Gallery to rearrange sheets in a section Selecting multiple sheets Check this option box below each sheet to select it Alternatively hold the Control key while clicking on several sheets D GraphPad Prism ares under curve pet Transform of Data 1 graph IA File Edit View Insert Change Arrange Window Help i ri sheet Undo Clipboas Analyes Change Acange Crew wees Text Expert Pret Send 28 A i 53 9 Fd Xw i9 Sawe K o Be EA a g d Family Search results p Deta wth Results ate T Data Ta
242. gs for that data set Click OK to redraw the graph with all the changes Note that a fitted curve is treated as a separate data set To change all data sets on the graph for example to make all symbols larger Click the Global button and choose Change all data sets Changes you make after that will then apply to all data sets Style With two grouping variable graphs replicates are placed in side by side columns on the data table One grouping variable is the main column heading the other is the row title 1995 2014 GraphPad Software Inc 246 GraphPad Prism User Guide Table format 44 33 33 44 ee ee ee ee a ee eee ee Choose how to display a data set on the graph Choose between a scatter dot plot an aligned dot plot a before and after plot a column or bar a box and whiskers plot or a floating bar showing the minimum and maximum 70 cak 60 E Dogs 40 40 0 20 10 0 S e e e amp Choose how to plot error bars Select SD SEM 95 CI or range Your style choice will determine which options below you can use Since it rarely makes sense to choose different error bar or replicate choices for different data sets you will probably want to click All before changing error bar format Format Symbols or bars If you choose to plot data as a scatter dot plot or a before and after graph select the symbol type size and color If you pick an open symbol also select a border thickne
243. h are not cloned For example say you have a data table analyzed with 1995 2014 GraphPad Software Inc 96 GraphPad Prism User Guide 7 3 a t test and graphed If you clone the graph the t test analysis will only be included if you have pasted a portion of the results onto that graph e To save the current graph as an example to clone in the future drop the File menu and choose Save Special Save as Example Start from a completed graph Don t erase the data before saving the example as you can ask Prism to remove the data when you clone the example e Can you clone layouts No But you can go to any layout and duplicate that sheet with its family e How is cloning a graph different than duplicating a family of sheets When you start from a graph and duplicate its family the results are identical to cloning that graph To clone a graph go to the Welcome dialog To duplicate a family go to the selected sheet Repeat analyses with the Wand If you ve already entered data onto an empty data table it is too late to clone too late to duplicate a family and too late to open a template at least without copy and pasting data Prism provides a great tool to solve this problem the Wand Wizard to ANalyze Data Use it to analyze and graph the new table just like you already analyzed and graphed an existing table Follow these steps 1 Start from the data table with data you wish to analyze and graph 2
244. h Settings Order of bars from left to nght or bottom to top for stacked bars WE First look grouped dataA Contro Data on graph First bok grouped data B Treatment FEST First look grouped dataC Treatment 2 Relation of selected data set with the previous one Interleaved Stacked Superimposed Grouped F Separate this data set from the pror one with a vertical ine 172 pt uo v Under data points Change Graph Type Hele Canc C aw C Order of bars within a data set The previous section explained how to adjust the order of the data sets The order of the individual columns within a particular data set is determined by the order they are entered in the data table Table format A B cats dogs AYI L AN2 I AN3 AN4 I ANS B71 J B Y2 I BY3 I 44 55 233 455 235 643 456 744 435 346 456 264 750 333 345 653 329 256 556 678 890 556 543 337 re en ee ee A a E aa a a a a aa a 1995 2014 GraphPad Software Inc 254 GraphPad Prism User Guide Food 1 Food 2 Food 3 To reverse the row order on a data table go to the data table From the Change menu click the Sort button and choose Reverse row order si E ae 0 223 Table format Food3 Food2 Food See another example of changing plotting order for Grouped graphs 14 3 4 Additional Grouped graph settings Graph Settings tab of Format Graph dialog Use the Graph Settings tab of the Forma
245. h a vertical line Thickness V2 pt ee Ga oo a 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends Empty columns An alternative way to leave a gap is to create an additional data set column on the data table enter only a single number usually 0 and include it on the graph If the baseline of the graph is 0 0 and that value is 0 0 then Prism will draw a zero height bar which is essentially a gap 14 2 3 Plotting order of Column graphs The two graphs in this example are identical except that the plotting order was reversed es885 88a F E Ff Z To reverse the plotting order of the data sets on a graph click the Rotate Flip b Change ei Le O To fine tune the left to right order go to the Data Sets on Graph tab of the Format Graph dialog 1995 2014 GraphPad Software Inc 234 GraphPad Prism User Guide g Format Graph Appearance Data Sets on Graph Graph Settings Data sets plotted left to right a Sample column data A Cortrol Data on graph i Sample column data B Drug A i Add a Sample column data C Drug B Replace Space between selected data set and the previous one 100 amp of normal Separate this data set from the prior one wth a vertical ine v Inde data poiri Change Graph Type Help Cancel apy Cok 14 2 4 Additional Column graph settings Graph Settings tab of Format Graph
246. han or equal to lt less than lt equal to greater than gt greater than or equal to gt or not equal lt gt to the value you enter It is not possible to define criteria that compare values in two columns only to compare the value in one column with a value you enter in the dialog Decimate If your data file is huge you can decimate the data as you import Decimate literally means to keep one of every ten rows of data but you can tell Prism to skip any number of rows between the rows it imports It imports a row skips the number of rows you specify and then reads another row This is useful with any large file as a way to make Prism files smaller and accelerate analyses and graphing Columns Choose a range of columns you wish to copy by specifying a first and last column Or choose to read a column skip one or more columns and then read another column Unstack Some statistics programs save data in an indexed format Sometimes called a stacked format Each row is for a case and each column is for a variable Different groups or experimental conditions are not defined by different columns as Prism is organized but rather by a grouping variable Prism can unstack indexed data Specify which column contains the data and which column contains the group identifier The group identifiers must be integers not text but do not have to start at 1 and do not have to be sequential Example In this sample of a
247. he ALL button just to the right Changes you make after that will then apply to all data sets Show Symbols Choose symbol type size and color If you pick an open symbol also select a border thickness Check the Clear option if you want point to point lines and overlapping points to show through the open symbol Use Shape the drop down menu to select one of Prism s symbols Use the More option on this 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 261 drop down to use any character from any font on your computer as a symbol Y Show symbols Color e Shape z Border color ME See 0060000 ize Enor bars BOPSOUFOe Color Di ch AVAVAAVY O56 0908 Cobor ME Pattem sti a 2p z Show area fill F d Connecting line Ey v In survival plots you can choose to show symbols only for censored data points or for all data points Make this selection on the Graph Settings tab of the Format graph dialog Error bars Choose how you want error bars to be formatted Error bars can go above or below a data point or in both directions Learn more about error bars on survival graphs Eror bars Colo E Thickness 1 pt X Connecting line Colo E Thickness 2p X Depending on the choices you made when you created a survival plot the option for error bars may or may not be available You can change this setting in the Graph Settings tab of the Format Graph dia
248. he All Ticks section To change the direction and length of ticks Double click on an axis to open the Format Axes dialog Set the direction and length of ticks in the All Ticks section To place additional custom ticks or grid lines on a graph See Additional ticks and grid lines 1995 2014 GraphPad Software Inc 284 GraphPad Prism User Guide 15 2 4 Graphs with a right Y axis When you plot several kinds of data on one graph it is often useful to plot some data using a Y axis on the left side of the graph and other data using a Y axis on the right side of the graph Note that you never can have more than one X axis 0 4 8 2S S a z 0 2 e Y v a O 04 D 0 10 20 30 40 50 60 70 Elution volume To create a second Y axis Double click on an axis to open the Frame and Origin tab of the Format Axes dialog Or click on the Format Axis tool in the Prism toolbar Change fi ul A KE i amp Select the tab for Right Y axis and choose how you want the axis to be formatted Format Axes Frame and Origin X anis Leftr axis Right Y axis Titles amp Fonts Autornaticaly deter NO Pi axis Range Reverse Two segments 4 Minimum Theee segments 4 l l Mavamum All data sets are initially graphed using the left Y axis Depending on the scale of the axis the data points may or may not all be visible 1995 2014 GraphPad Software Inc Graphs Frame and axes 285
249. he analysis unless you want two copies of the results To open the analysis parameters dialog click the analysis parameters in the upper left corner of any results sheet or in the toolbar Use the Learn and Analysis checklist buttons Click Learn from any Analyze dialog to learn more about the analysis Our help goes beyond program help and explains the principles behind the analysis Learn Once you ve finished any analysis click the Analysis Checklist button in the toolbar to make sure you are interpreting the results correctly Ea Paste results onto your graph Select any block of tabular results copy to the clipboard and paste onto any graph or layout This will be a live link If you change the data or the analysis choices the embedded results table will update Create chains of analyses without copying and pasting Many analyses i e Transform create results tables that can be used as a data table These results tables have green grids unlike tables with red grids that contain tabulations of results that cannot be graphed From any results table with a green grid click Analyze to analyze the results You can make the analysis chain as long as you want For example you could Transform then Normalize then fit with Nonlinear regression then transform the residuals from the regression Exporting tips Use the Send to Word and Send to PowerPoint buttons 1995 2014 GraphPad Software Inc Getting
250. he loop also starts the next row on the table When the loop is complete so is the table In rare circumstances you might not want the end of a row to correspond with the Next statement of a loop In this case end a row with the NextRow statement and close the table before the loop ends with the EndTable statement 23 2 17 Writing to text files Commands OpenOutput filename lt CLEAR gt lt delimiter gt WText lt text gt lt amp gt WDate lt amp gt WTitle WCell row col lt subcol gt lt amp gt WRow row lt col gt lt subcol gt lt amp gt WCol row lt col gt lt subcol gt lt amp gt WSheet lt row col subcol gt lt amp gt WBlock row s column s lt row label gt lt gt WTCol row col lt subcolumn gt lt amp gt WTRow row lt col subcol gt lt amp gt WTSheet lt row col subcol gt lt amp gt WTBlock row s columns to include lt row label gt lt gt WVersion CloseOutput Explanation Prism offers two methods for writing results froma script The previous section explains how to write tables A more general method writing to a text file is explained here Generally you ll find it easier to write to tables previous section but may find uses for the extra flexibility of writing to text files 1995 2014 GraphPad Software Inc 434 GraphPad Prism User Guide The first step is to use the OpenOutput command to open or create a fil
251. he range and interval of the example graphs 13 7 Color schemes Color schemes change all of a graph s colors at once They are very useful but underused Go to the graph you want to change or select several graphs in the gallery Then click on the Color Scheme button in the Change section of the Prism toolbar You can choose the Black and White or Colors schemes right from the menu or click More Color Schemes to have more choices 1995 2014 GraphPad Software Inc 200 GraphPad Prism User Guide Cnange Arrange Uraw write iL it e a ahe K ly el O TH a Aa B Cnr Black and White Colors 2 More Color Schemes Set the Default Color Scheme Background b Plotting Area b Axes gt In the color schemes dialog you can choose a color scheme by name using the drop down menu or use the arrow buttons to browse the schemes Color Scheme dose response NIND inhibi 1 10 percent maximal response o 610 10 107 106 10 104 10 agonist You are not limited to the color schemes we provide To create a new color scheme start from a graph with the colors you like Click the Color Scheme toolbar button and choose Define Color Scheme 1995 2014 GraphPad Software Inc Prism Graphs the basics 201 13 8 Selecting colors Mac To change colors individually without dealing with color schemes e Change the color of a data set in the Fo
252. he results tables This means that results tables embedded on graphs may no longer show the results you care about and scripts may export the wrong values You may have to do a bit of clean up to make the files work as intended File compatibility between Windows and Mac Prism files The Windows and Mac versions of Prism use the same file format and you can go back and forth without any special conversion Compatibility of Prism objects saved within other documents On Windows but not Mac when you paste a Prism graph or layout within Word or PowerPoint or some other programs you can paste just a picture paste a link or embed a Prism object If you paste a link or embed an object you can then double click on that image to edit within Prism This works only if the correct version of Prism or the free Viewer is installed If a Prism 5 object is embedded within a Word document for example double clicking to edit that object will only work if Prism 5 or later is installed on that computer Double clicking on a Prism 4 object will open Prism 4 if it is present on that computer or Prism 5 or 6 if Prism 4 is not present 8 3 Backing up Prism files Automatic backups 1995 2014 GraphPad Software Inc 104 GraphPad Prism User Guide Choose automatic backups on the File amp Printer tab of the Preferences dialog and Prism will automatically save your work Choose to save based on a timer every few minutes and or whenever y
253. he table with a subcolumn labeled for SD values Don t make changes in the Format Data Table dialog when you want to change the way the error bars are plotted Read on to see how to change error bar plotting Choosing how the replicates or error bars are plotted When you create a new table and enter replicates you choose not only how the subcolumns are formatted but also how Prism plots them You can choose to plot individual replicates mean only mean with error bar which you can specify Choose all this right under the spot where you choose the number of replicates If you choose to enter error values directly Prism will plot the values you entered except that when you enter CV Prism plots the SD If you entered Mean SD or SEM and N you can choose on the graph to plot the error bars as SD SEM or 95 Cl Changing how replicates or error bars are plotted To plot the replicates or error bars differently you don t have to remake a graph Instead click the Change graph type button Change GLE LS a N aha amp The changes you make on the Change Type of Graph dialog apply to all data sets on the graph An alternative approach is to double click anywhere on the graph to bring up the Format Graph dialog Then click the All button so changes you make apply to all data sets If you don t do this you might accidentally end up with some data sets having one kind of error bar and other data sets with a different kind o
254. hibitor HEE Best ft vakes H a Std Eror 8S Lower 95 confidence imit b ais Upper 95 confidence imit We Dependency 2 Goodness of Fit IB inhibitor 1 10 H A Best fk values 2 Std Eror gt Lower 95 confidence imit SE Upper 95 confidence imit BE Dependency H A Goodness of Fit 5 H Global shared 2 Goodness of Fit Degrees of Freedom 25 00 R square 0 9783 yF Adjusted R square 0 9775 7 Absolute Sum of Squares 819 7 oF Sym 5 726 9 Degrees of Freedom 27 00 i7 R square 0 9724 JE Adjusted R square 0 9714 F Absolute Sum of Squares 1223 FF Syx 6 730 Example 1 QC plot 1995 2014 GraphPad Software Inc 2SD 2SD Measurement 0 5 10 15 20 Run Number The graph shows repeated quality control measurements The column statistics analysis was run to compute the mean and SD and more of the values The lines at the mean and plus or minus two standard deviations were drawn by hooking these values This means that the grid lines will move as more data are entered into the data table First double click on the Y axis to bring up the Format Axes dialog on the Y axis tab The bottom of the dialog lets you add additional ticks and grid lines To hook the grid line to an analysis constant requires drilling down to the details dialog so click the button 1995 2014 GraphPad Software Inc 33 GraphPad Prism User Guide r Format Axes Gaps and Director Standeed
255. his is quite rare but easy to work around One way to get Prism to stop check for updates is to use the U switch when starting Prism Edit the Prism start icon so that the target looks something like this with quotes around the path but not around the U and a space beteween the quotation mark and the slash C Program Files GraphPad Prism5 prism exe U Create startup log L If Prism will not start at all it can help to create a start log This will show us which steps Prism completes successfully and which steps fail To create a start log edit the Prism start icon to add the L switch so the target looks looks something like this with quotes around the path but not around the L anda space between the quotation mark and the slash C Program Files GraphPad Prism5 prism exe L Regenerate PZE files prism equations cache E The built in equations are actually installed as a set of Prism files You can even add your own built in equations The first time Prism runs it compiles these equations to a form PZE files that it can access and compute very quickly It should never be necessary but you can force Prism to compile all the equations again To do so edit the Prism start icon to add the E switch so the target looks something like this with quotes around the path but not around the E and a space beteween the quotation mark and the slash C Program Files GraphPad Prism5 prism exe E Print file P
256. hmic and the other isn t When both axes are logarithmic the graph is called a log log plot 15 3 2 How to Create a log axis This page shows how to stretch the axis to a logarithmic scale which doesn t alter your data Distinguish this from transforming your data to logarithms which you can plot To create a log axis Double click on the axis to open the Format Axes dialog In the Scale section set the axis to Log10 or Log 2 This graph shows log spaced minor ticks The minor ticks between the major ticks at 10 and 100 show the position of 20 30 40 50 60 70 80 and 90 Since the minor ticks are not equally spaced on the graph we call these log spaced minor ticks Note that there are eight ticks so nine intervals many people mistakenly think there ought to be ten 1995 2014 GraphPad Software Inc Graphs Frame and axes 305 1750 a d a on QA oases co co e 750 500 2504 Specific Binding cpm o mammann iii m ee ee 1 10 100 1000 Radioligand nM To set the numbering for a log axis Double click on the axis to open the Format Axes dialog and set the number format in the Numbering or Labeling section Prism offers three numbering format choices for log axes Antilog 10 100 1000 10000 etc Scientific 1x10 1x10 1x10 1x10 etc Power of 10 10 107 10 10 etc Log 1 2 3 4 etc To set the minor tick intervals for a log axis Double click on the
257. hoose to start with a blank screen or to start with a copy of an existing script A 3 GraphPad Prism Script Attached script Monte Carlo simulations Script log Script syntax Your script Script syntax Morte Carlo analysis a nP h required argument efore running this script you must have op eae peoject with the folowing i optional argument gt i The frst sheet in the results sections a _ P data simulation 7 comment y The second sheet in the results section is multiple regression curve fit of the samuated data line The first data table in this fle must be fon ts one way table and be blank comments The sample script below contains some info Simulations brackets like thes You need to replace the m placeholders including the beackets before ForEach of loops the script Regenerate X Next 4 m t Beep X Step through script Edit Script Automatically tun this script 1 Step 12 Steps Save Delete Script Every time this file is opened Every time this file is closed 4 Enter or edit the script on the left side of the GraphPad Prism Script dialog Use the right side to review script syntax 5 Repeatedly click 1 step to step through the script You can watch the result in Prism as well as observe the script log 6 Click 12 steps if you are feeling lucky 7 Click Run when you are convinced the script will run without error The Script dialo
258. ht With TIF format and no other Prism lets you choose to compress the file The advantage of compressing of course is that the file is smaller The disadvantage is that compressed TIF files might be less compatible with other programs With Prism Windows but not Mac choose between two compression methods PackBits compression create the smallest file size but LZW Lempel Ziv Welch compression might be more compatible Prism Mac does not offer you a choice of compression methods It uses LZW compression when you chose Grayscale CMYK or RGB millions of colors 16 bits and PackBits compression when you choose Monochrome or RGB 256 colors 8 bits Previous versions of Prism Mac included an alpha channel when exporting in TIFF format and this caused problems with some journal production systems Prism 6 does not include this alpha channel EMF or WMF Windows only Windows Metafile WMF and Extended metafile EMF files contain vector and font instructions for how to draw the graph This means you can resize the image in another program with no loss of quality These formats are only used by Windows program not Mac programs and Prism Mac cannot export in these formats 1995 2014 GraphPad Software Inc GraphPad Prism User Guide WMF or EMF EMF is newer and better in theory but some programs work better with WMF If you have problems with one setting try the other You can set the default for how Prism copies gr
259. ht click an the data point and choose Format The Point Remove all the indvidual formatting Revert all data ponts to the format of thei data sets One point has individual formatting Gaps at missing points Leave a gap when you have missing data points or connect the existing data points on each side Effect of GP 41152 on Receptor Number Effect of GP 41152 on Receptor Number PTYTTINTITETTINITINITINTTIRTTI LITT TTT TTT soo Bmax Ma weccdccce coco cece ceccmces ceccmeces cocmeccs coos cece cescaece t 750 oe oe E g 500 4 BMAX 993 8 4 BMAX 993 8 250 KO 2 818 250 KO 2 818 i 0 KD 5 10 15 20 Oo KO 5 10 15 20 PH Yohirbine nM PH Yohirbine nM Reset any individual formatting of points or bars If you have changed the format of individual data points by right clicking on them check an option here to reset everything back to the format set in the dialog 1995 2014 GraphPad Software Inc 2 4 GraphPad Prism User Guide 14 2 Column graphs Bar formatting and spacing Format graph Column Prism lets you change every feature of a graph Change the shape color and size of graph symbols change the fill pattern and color of graph columns change the order that data sets are plotted Double click on any symbol or bar or the background of the graph to bring up the Format Graph dialog See also Appearance of Column graphs Data set spacing on Column graphs Plo
260. ht type of graph Prism 6 no longer asks you to pick the graph type on the Welcome dialog which leaves the Welcome dialog less cluttered and easier to understand Instead you choose the graph type the first time you view a new graph Choose a graph type by choosing among a set of icons and preview how that kind of graph looks with your data 1995 2014 GraphPad Software Inc 22 GraphPad Prism User Guide e Format several data sets at once The Format Graph dialog in Prism 5 always let you either change one data set at a time or click the all button to change all data sets at once Prism 6 also lets you choose a defined subset of data sets at once For example you could select data sets A C E and G and change all of those data sets to use a dotted line Then choose B D F and H and make those lines solid e Click the apply button to see changes without closing the Format Graph or Format Axes dialog The Format Graph and Format Axis dialogs are very powerful and give you a huge number of options to change the appearance of your graph To avoid the need to click OK then go back to the dialog to make more changes simply click the new Apply button and you ll see the effect of the changes you made without closing the dialog e View graphs faster An XY graph with many points appear on screen faster when you switch to it and is regraphed much faster after you make any changes in the Format Axes or Format Graph dialogs or if you mo
261. ice does not apply to Prism Mac Changing this setting can help problems in copying and pasting graphs to other applications Note that when you copy and paste between Prism and Microsoft Office applications like PowerPoint and Word you may get better results using EMF or WMF There s really no way to predict which will work better If you re having problems try setting another format as the default choice for copying and pasting You can also specify how Prism will format decimal separators excluded values and the background colors of graphs and layouts Copy to clipboard Copy graphs and layouts as EMF only z Background color Omit Make the pasted background c w Copy excluded values Numbers followed by z Decimal separator System default from Control Panel v Graph tab e Set defaults for axes error bars symbols and lines color schemes and graph and data table fonts Analysis tab e Set defaults for linear regression nonlinear regression weighting and whether or not to create new graphs from transforms normalizations pruning baseline removal etc Internet tab e Set default FTP connections logins and settings Info Sheet tab 1995 2014 GraphPad Software Inc Organizing Prism projects 91 e Set default headings to include on newInfo Sheets File locations tab e Set default locations for saving files backups templates scripts etc Choose to set specific directories or
262. idual preference files Prism stores the list of user defined equations choices from the Preferences dialogs the list of recently used files and more in a configuration file Prism Windows stores preferences in the file Prism6 cfg Prism Mac stores preferences in a file named Prism6 Preferences The location of these files depends on which version of Windows or the Mac OS you use so search for them If several people use the same Windows computer each may wish to maintain their own preferences and equations To do this create a different shortcut icon for each user In the target portion of the properties dialog for the shortcut enter the full path name of the Prism program followed by O letter O not zero and then the full name of the configuration file you want to use If the file doesn t exist Prism will create it For example C Program Files PRISM5 PRISM EXE OC JERRYS JSPRISM CNF If you are running a network license you may place the Prism6 cfg file into the program folder on the shared server drive When Prism is first used on a new computer it will use the settings in this shared configuration file Changes will be saved on the individual user s hard drive This means that all users can begin with the same settings but then customize them 24 3 Shared templates methods and examples You can ensure that everyone using Prism sees the same templates methods and examples Create them on one c
263. ifference between entering errors and upper lower limit errors It is easy to confuse the and upper lower choices for entry of preaveraged data But the two are distinct e When you format the subcolumns for entry of error values the values you enter are interpreted as distances These are added to or subtracted from the value you enter as the mean to compute the end point of the error bars e When you format subcolumns for entry of upper lower Limit error values the values you enter are interpreted as the end points of the error bars The error bars will end at the Y values you enter What if want to enter the median and quartiles or some other kind of error bars If you choose to enter the mean with sample size n and SD SEM or CV you really ought to enter those exact values Otherwise analyses might be incorrect 1995 2014 GraphPad Software Inc 156 GraphPad Prism User Guide 11 9 If you choose to format the data table with subcolumns for Mean and SD or SEM or CV without sample size or for mean with error values or upper and lower limits no analyses will be possible Or rather Prism will only analyze fit the means and ignore the error values If you choose to format the table so the subcolumns are labeled mean upper limit and lower limit you are welcome to enter into those subcolumns the median plus the 25th and 75th percentiles or whatever values you want Prism will plot the error values y
264. ilar to logarithm logit and logistic The term ogistic sounds like it is related to logarithms In fact the term logistic has three distinct meanings which don t all involve logarithms The ogit function used in logistic regression is the natural logarithm of a probability P with a value between 0 0 and 1 0 divided by 1 P Logit P In P 1 P The ognorma distribution is a distribution of values whose logarithms follow a Gaussian distribution The lognormal distribution itself is asymmetrical with a heavy tail to the right It is easy to be mislead by the asymmetry and mistakenly eliminate values in the tail of the distribution as outliers The notation log x can be ambiguous Within Prism transforms and equations the log function computes the common base 10 logarithm With some computer languages for example Javascript log x denotes a natural logarithm not a common logarithm Excel is especially confusing In an Excel worksheet function log X is the common logarithm but in an Excel VBA macro log X is the natural log The notation In X is the natural logarithm in Prism 16 Analyzing data with Prism 1995 2014 GraphPad Software Inc Analyzing data with Prism 317 This section explains how to analyze data with Prism For help with statistical principles and with particular analyses go to the Statistics Guide 1995 2014 GraphPad Software Inc ss GraphPad Prism User
265. im versions as you work Expand all tips Collapse all tips 4 8 Differences between Windows and Mac versions We work hard to keep the Windows and Mac versions of Prism very similar You can switch back and forth between platforms easily and files created on one platform can be opened on the other But there are a few differences Features in Windows but not Mac e Object linking and embedding This means you can paste a Prism graph into another program and double click to edit in Prism e Excel linking and embedding This means you can paste Excel data into Prism and double click to edit within Excel e Audio notes can be embedded on graphs or layouts e Import and export EMF and WMF images e Send to Word with a single click e One click to post a graph or layout on a web site e High contrast printing with no grays and no colors choice on Preferences dialog e Visual Basic for Applications VBA commands to launch Prism and start a script e Find Prism files using Google Desktop Search e Export in the older PCX format Features in Mac but not Windows e Spell checking of text anywhere in the project 1995 2014 GraphPad Software Inc GraphPad Prism User Guide e Quick Look lets you preview graphs within Finder e Color eyedropper While setting any color click the magnifying glass tool then click on any color on any window to select that color e Use an Automator action to launch Pri
266. inate or text of an additional tick can be hooked to an analysis constant or info constant Click on the Details button in the Additional Ticks and Grid lines section and then on the Hook icon in the Format Additional Ticks and Grids section and select the constant you wish to link to 1995 2014 GraphPad Software Inc 2 GraphPad Prism User Guide AY F Show Text Text line 1 Kd Text line 2 Location E Show Tick Size Drechon Auto V Show Grid Line Thickness Color Fill shade between this tick and Y f Oe Coe Patter Fil color Under data points X 1995 2014 GraphPad Software Inc Graphs Frame and axes 297 f OB kuik Contant Choose a value from an info or analysts constant This wil be a hot 1 link to be automatically updated in the future Gib Analysis constants i 5 Fa Nonlin fit of Specific binding data 3 Specific bindin Gg Best fit values Bmax 1338 BE Std Ero ig Lower 95 confidence limit gE Upper 95 confidence limit aa Dependency zA Goodness of F 1500 BMAX D EZ 1000 m o gt ee S gt 500 OKD 10 20 30 40 nM Radiolgian In this example the dashed line for Kd and BMax were hooked to the Kd and BMax 1995 2014 GraphPad Software Inc 298 GraphPad Prism User Guide values in fit by nonlinear regression If the raw data are subsequently changed both
267. indows only 1995 2014 GraphPad Software Inc Importing and exporting data 173 Paste or Import the selected data into the data table and also paste a copy of the entire original spreadsheet or text file into your Prism project even if it has several worksheets tabs This means you don t need to worry about keeping track of multiple files You don t need to save the spreadsheet file separately except as a backup You can open Excel from within Prism edit the data and instantly update the analyses and graphs in Prism A potential disadvantage of embedding is that you will end up with multiple copies of the same data Another disadvantage is that your Prism files will be larger Automatically update Prism when the data file is changed If you check this option whenever you look at a Prism data table graph results sheet or layout Prism will update the sheet if the linked Excel file has been changed Excel options What Excel puts on the clipboard Excel Windows 2003 and Excel Mac 2008 copy data to the clipboard in two formats Plain text and HTML Numbers a Mac spreadsheet that is part of iWork only copies in plan text format When there is a choice Prism starting with 5 0c and 5 03 pastes the HTML format by default This allows much better pasting of Greek letters superscripts and subscripts titles with punctuation numbers with nonstandard thousands or decimal separators and more You can specify that the text f
268. ing choices When compressing TIF files choose between the LZW or packbits scheme Choose either a RGB or CMYK color model for PNG files Choose higher resolution output up to 1200 dpi with JPG e No popup dialog after exporting After exporting a graph layout or table Prism 5 would always pop up a dialog offering to open the folder to which the file was exported When it is done exporting Prism 6 doesn t show that extra dialog Instead Prism 6 lets you choose in the export dialog whether to open the folder after exporting You can make that choice a default for the future e More importing choices Prism 6 Windows can import more kinds of images onto a graph or layout Here is the complete list Windows Enhanced Metafile emf Windows Metafile wmf TIFF tif tiff JPEG jpg jp2 j2k jpx Portable Network Graphics png mng Windows Bitmap bmp Graphics Interchange Format gif Scalable Vector Graphics Format svg PC PaintBrush pcx TruvisionTarga Format tga Microsoft Paint Format msp PhotoShop 3 0 Format psd Windows Icon and Cursor Formats ico Macintosh Pict pct pict e Choices when copying excluded values Prism lets you exclude values on the data table where they appear in blue italics These values are ignored when Prism makes graphs and analyzes data Prism 6 offers three choices for how excluded values should be copied or exported 1 Like other values ignoring th
269. int use the right click menu You can also change all the symbols in selected data sets Double click on any graph symbol or bar to open the Format Graph dialog r Format Graph Appearance Data Sets on Graph Graph Settings Data set _ form of Dose response data experiment 1 no inhibitor bd m Global Style Appearance Mean and Esror Plt SD X J Show symbols f Cobr E Shape E ae See 4 og X t Show bars spikes droplines Duon eee J Show error bars Color GE Di Above v Style T v Thickness 1 pt Show connecting line curve aes tart Ine at origin One line for each subcolumn Show area fill es v Additional options a Piton Leit Y ans Show legend Symbol amp Line X Right Y axis Revest legend to column title Label each point with ts row tithe Change Graph Type Help Cancel Appy OK To change the settings for one data set Select a data set from the list and choose the symbols lines and error bars for that data set Then select another data set and choose settings for that data set Click OK to redraw the graph with all the changes Note that a fitted curve is treated as a separate data set To change all data sets on the graph for example to make all symbols larger 1995 2014 GraphPad Software Inc 24 GraphPad Prism User Guide Click the Global button at the top right of the Format Axis dialog Then choose to change all data sets or a s
270. inted exported copied to clipboard or used as a Magic example so long as it had been saved so the file has a name 1995 2014 GraphPad Software Inc 198 GraphPad Prism User Guide You have abeady selected the gaghis that wil be changed Now choose the graph to serve a an example v bar demo_pef n C Users Geoff Dropbox fikes slideshow pzf files en Click Next and then select the properties of the example graph you would like to apply to your current graph or graphs 1995 2014 GraphPad Software Inc Prism Graphs the basics 199 X Magic Step 2 Choose properties of example graph to apply wt Example graph Ongnal f a ee ote mpera a 3 AN nd s e lt 4 E i Zz e gg ng ae ae Range and tchs of aes Wath changes r o e e Addbona icke amp gid ines with labe nero 119 7 Agpesance ol sybols bars etc dose response How to change several ga r a ance Help Cancel lt lt Back _ OK J j If you check the option Range and ticks of axis what Prism does depends on whether you have checked the option to use an automatic range for the axes If that is checked on the example graph then Prism will check that option on the graphs you are changing Depending on the range of the axes they may or may not end up with the same range If that option is not checked on the example graph then all of the graphs you are changing will be changed to have t
271. intigecebasieneh Error bars and replicates Key concept Replicates and error bars Replicates and error bars on XY graphs Replicates and error bars on Column graphs Replicates and error bars on Grouped graphs Stacked vs side by side replicates Error bars and confidence bands on Survival graphs Confidence and prediction bands from regression Graphing error bars calclated elsewhere Graphing each replicate sseeeeeeeeeeees Importing and exporting data Key concept linking and embedding data Paste linking data from Prism Pasting data from Excel Windows Pasting data from Excel Mac Options when pasting data from Excel win or mac Importing data from text files Importing text and Excel files directly Importing and pasting choices Source fa Do aaee a ea a Ake View tab Asnar reae iari 1995 2014 GraphPad Software Inc Contents 5 10 11 12 Part XIII O AN Oo RP WN a _ gt _ gt 12 Part XIV 1 Filf ritab iiare a aa aE aaa a eis ahesence stesaarsievsdes nus uedeesesvoeucee 175 Place me nt tab irssi aeaaea iaaa aa aaa dee aeeteneaneten saves soeeauenvaneianeeesuede 177 Mfo g Notes tab osc E a i ccctees a aE a a a a piv EE S aaa 179 Troubleshooting Negative numbers become positive fractional numbers become integers PE AT S T A E A OTT 181 Unlinking data obj cts iiinis iaeaea i aA e A aar aa iaae ea aaae 182 Changing linked and embedded data
272. ints Show meanas Border 2 pt X There are seven ways to plot box and whisker graphs Traditional Tukey whiskers go 1 5 times the interquartile distance or to the highest or lowest point whichever is shorter Other choices show specified percentiles which seems more logical Any data beyond these whiskers are shown as points Or you can choose to superimpose each individual point on the box and whisker plot Because whiskers can be done in various ways it is essential to mention in a graph s figure legend which way they were made Bars and boxes Set the format of bars and the box part of box whisker plots Note that if you choose the first selection in pattern the bar will have a solid color chosen in fill Symbols Choice here apply to symbols used for column scatter and before after graphs as well as the symbols shown if any on box and whisker plots If you check the option to plot a symbols on a bar graph every value will be plotted If you check the option top plot symbols on a box and whiskers plot the number of symbols is chosen in the drop down in the Style section see above You can choose to plot all points last choice in the list or only to plot outliers defined in various ways Error bars Choose the format and color of error bars Learn more about error bars on Column graphs Lines 1995 2014 GraphPad Software Inc 228 GraphPad Prism User Guide Choose the color and thickness of lines fo
273. ion curve fit Linear regression Fit spine LOWESS Smooth dilferentiate o integrate curve Area under curve Deming Model I linear regression Column stabshos Row means with SD o SEM Correlation interpolate a Standard Curve Column analyses Grouped analyses Contingency table analyses Survival analyses Parts of whole analyses X HEEEL Deselect All Results will appear on a new results page with a green grid While you cannot edit these results you can create a new graph use the New button and do further analyses click the Analyze button To help keep track of chains of analyses use the Data Results folder in the Navigator What if Prism doesn t offer the tools you need to manipulate your data In that case you should enter and manipulate your data in Excel and then copy and paste the results into Prism for further analysis and graphing Note that you can paste a link to the Excel file or you can paste embed the entire Excel workbook within Prism Learn more about linking and embedding data from Excel 1995 2014 GraphPad Software Inc 348 GraphPad Prism User Guide 18 2 Transform data When you transform data with Prism the data table isn t changed Instead Prism creates a new results table with the transformed values a Standard functions Choose a function Choose from one of these functions for transforming Y values analogous functions are available for X Function Y Y K Y K Y K Y
274. is designed to cease to function upon expiration of the term of your subscription if the subscription is not renewed and iii you may generally renew your subscription but the terms upon which the Software may be licensed upon a renewal are subject to change by GraphPad at its sole discretion Any attempt to defeat the time control disabling function in the Software is a material breach of this Agreement and a violation of intellectual property law d A group subscription license lasts for the period of time for which you subscribed as indicated on your invoice for the Software and may only be earlier terminated by GraphPad if you violate the terms of this Agreement Your subscription is to activate the software on an authorized number of computers Upgrades to newer versions during the term of the subscription are included You acknowledge that i your right to install and use the Software is limited to the term of your subscription ii the Software is designed to cease to function upon expiration of the term of your subscription if the subscription is not renewed and iii you may generally renew your subscription but the terms upon which the Software may be licensed upon a renewal are subject to change by GraphPad at its sole discretion Any attempt to defeat the time control disabling function in the Software is a material breach of this Agreement and a violation of intellectual property law e The license for the free Prism Viewer does
275. ism be sure not notice these four unique aspects of Prism e Organized data tables e Everything is hot linked e A complete record of your work e Helps you learn data analysis 3 1 Organized data tables Formatted data tables simplify graphing Unlike spreadsheet programs and other scientific graphing programs Prism s data tables XY are structured or formatted Whenever you create a new data table choose one of six Grouped table types This makes it much easier to create appropriate graphs and to eae choose suitable analyses Column Contingency Parts of whole Enter SD or SEM values computed elsewhere If you computed error values Group A Table format Control elsewhere enter them onto Grouped rrena labeled SD or SEM F x Mean SD N Mean SD N subcolumns Prism s analyses 1 Wild type 21 00 200 81 33 15 63 i e t test ANOVA regression Knock outA 2350 0 71 30 67 1 53 3 Knock out B 24 33 3 06 68 33 3 06 will take into account the SD or SEM and sample size Create error bars from raw data 1995 2014 GraphPad Software Inc How Prism is unique 39 X Minutes Group A Control AYI AYZ AY3 8887 7366 961 8329 7907 Enter the raw data i e triplicates and Prism will automatically compute and plot the error bars You can instantly switch between plotting the raw data or plotting mean with SD SEM confidence int
276. ism double click on the program icon It is not possible to launch more than two instances of Prism Opening two distinct Prism windows is new to Prism 6 Once you have a second copy of Prism running you can open any file within it If you open a file that is already open in the other copy instance of Prism then you won t be able to save any changes unless you use File Save As and choose a new file name Any changes you make in one instance of Prism will not be seen in the other Use the second launch of Prism to view one sheet say a page of results while you edit another sheet the graph in the original launch of Prism The Windows menu of each instance of Prism will only show files open in that instance Prism Mac There is no concept of a parent or overall Prism window when you use Prism Mac Each project file you open or create is in its own window You can move each project to whatever display you want The Windows menu lists all open Prism projects 5 8 Tips for working in a small window Working on a small screen can be difficult To free up space to have more working space e With Prism Mac starting with 6 0c if you are using Lion or later you can click a button at the top right of the toolbar to run full screen When you use the View menu to view or hide the top toolbar the navigator and the bottom toolbar those choices will apply only to the full screen view You can make different choices for when the Prism window
277. ith box whiskers a GraphPad Prism User Guide subjects Row and column titles e Write two or three line titles e Use bold and italics e Make titles as long as necessary e View and edit all of your column titles at once Work more efficiently Faster in many ways saving graphing exporting and closing Nonparametric calculations are way way faster Separate columns with lines Format several data sets at once Want to plot alternating columns as dotted lines Now you can do it in one step Paste link data or results copied from Prism and those ry values will be hot linked o 2 3 z Choose the size shape and color of selected data points right from the data table More choices when exporting Set defaults as you work Many dialogs now a have checkbox to make your choices on that dialog or tab become the defaults when you use that dialog in the future Much easier to create the graph you want since you don t pick the graph type until after entering data Preview how different graphs look with your data before deciding Search a large project to find pages that include specified text Label both sides of an axis 2 2 What s new Statistics Repeated measures ANOVA e Two way ANOVA with repeated measures in both factors Prism 5 could only compute two way ANOVA with repeated measures in one of the factors Prism 6 can handle repeated measures in both factors e More subjects Prism 6 now allows up to 256 subcolumns s
278. itional ticks and grid lines AtYs Tick Fonts Greek Details 5 oO L J Show additonal ticks With regula ticks Instead of regular ticks Only regular ticks 15 2 2 Axis numbering or titles Double click on an axis to open the Frame and Origin tab of the Format Axes dialog Or click on the Format Axis tool in the Prism toolbar 1995 2014 GraphPad Software Inc Graphs Frame and axes 281 hange Gi a ON K amp What values or labels show on the X axis XY graphs Normally of course the X axis of an XY graph plots the X values you enter into the X column The X axis in this case is numerical If the X values are not evenly spaced then the points won t be equally spaced If you enter row titles for each row then you can choose to label the X axis with row titles rather than X values Choose in the Number format drop down in the Regularly spaced ticks part of the Format Axes dialog Format Axes Frame and Origin Xaris Lett Y axis RightY axis Titles amp Fonts Gaps and Drecton Standard Scale Linear x Automatically determine the range and interval Range row numbers Mnmum Maimun All ticks Ticks direction Down Location of numbenng labeing Below hoizontal Ticks length Short Numbering labeling angle Regularly spaced ticks Mace ticks terval Number format Prefix Starting at X omnes Decimals Decimal Suffix Scientic Mince ticks
279. itles Automatic column widths x Enter X values Also entes X error values to plot horizortal esoe bars Generate X values a a seres darting at 000 inincremerts of 1 01 Y Enter and plot a single Y value fo each point Enter 2 rephcate values in side by side subcoluenne Ente and plot error values calculated elsewhere Enter Mean SD N z Help Cancel OK If you want to change the type of error bars displayed on your graph you don t need to change the data table Instead double click on any data point on your graph to open the Format Graph dialog and use the drop down menu to change the error bar format 10 4 Choosing a table to create a bar graph Prism offers six distinct types of data tables Four of these can be used to create bar graphs as detailed below If you want to create a bar graph it is important to choose the kind of data table that matches your data Column graphs Enter data for each group into its own column stacking replicates if any Each column then becomes a bar and you ll be able to control the appearance of each bar individually 1995 2014 GraphPad Software Inc Data tables 125 Group A Group B Group C Grou Cats Dogs Mice d Y Y Y Y EF 13 2 1 12 15 24 1 2 wf om on af wf nl a 25 20 15 10 Cats Dogs Hamsters Note If you want to create a graph like the one above but you ve already calculated your mean and error values start instead with a Groupe
280. ks Ticks dtection Down Location of numbering labeling Below angled Ticks length Short m Numbering abeling angle 4S Regularly spaced ticks Mayor ticks ntervat Number format Column titles Flow bhes Row numbers Starting at X Decimals Minor ticks Thousands Other types of graphs Survival graphs always use Survival time as the X values Column graphs always label the X axis with column titles Parts of whole graphs don t have axes Appearance of axis numbers or labels To change the font size and color of the numbering for one axis Go to the Titles and Fonts tab of the Format Axes dialog Click the Font button in the Numbering or labeling section Or select an axis by clicking on it and use the Font settings in the toolbar To change the default font used for new graphs Set on the New Graphs tab of the Preferences dialog To move the numbers above below the X axis or to the right left of the Y axis Select the position of the axis numbering in the Axis Titles section on the Titles and Fonts tab of the Format Axes dialog Or select the axis numbering by clicking once then drag the numbering with the mouse or nudge it by clicking the arrow keys To put a prefix in front of all axis numbers or a suffix after Enter the prefix i e or suffix i e in the Format Axes dialog To rotate the numbering 90 degrees 1995 2014 GraphPad Software Inc Graphs Frame and axes 283 Set the numbe
281. l D Nudge The set of objects now acts as a single object If you want to work with the individual objects again drop the Arrange menu and choose Ungroup 20 6 Aligning objects on a graph Automatic snapping Prism will automatically try to snap objects to be in alignment with graph axes and other objects For instance you can drag a text box over a bar or group of bars and Prism will try to snap the text box to align with the centerline of the bar Prism will also change the justification of the text to centered If you don t like this you can change the justification back using the text justification button in the Text toolbar To overcome this automatic snapping hold down the ALT Windows or Option Mac key while dragging the object 1995 2014 GraphPad Software Inc 380 GraphPad Prism User Guide Note increase CI Dogs EB Cats Hamsters Day1 Day 10 Day 20 Day 30 Using the Align or Group button in the Arrange section of the Prism toolbar For graphs use the drop down menu under the Arrange button p wee S Change Arrange Draw Write Text it amp pa va w Q g ni i ii Center on Page Send to Front Send to Back Group Lock Object Duplicate Object no inhibi inhibitor 1 Ctrl D tion Object Nudge For layouts each task has its own button in the Arrange toolbar Arrange a A m S 2 m To align objects 1
282. l adjust accordingly Click on any label on the graph and use the Text section of the Prism toolbar to change the size font and color of all the labels x Group A 30 Gv MIJ Days Cats 25 HM X A Y1 A Y2 gt 20 ps 1544s 5 13 10 1 1 5 15 12 15 0 2 12 11 0 5 10 15 20 25 14 1 2 Front to back order of data sets When data points overlap or are superimposed on an XY graph the plotting order determines which will show on top The two graphs in this example are identical except that the plotting order was reversed Note the green symbols are behind the clear ones in the graph on the left and in front on the graph on the right Signal Signal 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 219 To change the front to back order of the data sets on a graph Click the Rotate Flip button in the Change section of the Prism toolbar to reverse the front to back order of data sets on a graph fi L Boy KB it Be To fine tune the front to back order go to the Data Sets on Graph tab of the Format Graph dialog A Format Graph Appearance Data Sets on Graph Graph Settings The order of data sets in thes list determines what happens when two data points overlap Data sets placed higher on this list will be graphed in font of data sets lower on the list Data sets plotted front to back ponse data experiment 1 Curve B inhibtor 1 10 Data on graph espon
283. lbar 2 On the first Fit tab choose the folder Dose response Stimulation Then 1995 2014 GraphPad Software Inc 340 GraphPad Prism User Guide choose the equation log agonist vs response Variable slope You can accept all the defaults for the other tabs 3 Click OK and Prism will fit the model to the data and graph the curve on the graphs Step 3 Simulate a few more data sets Note the Hill Slope the parameter we wish to investigate in this simulation To simulate new data with different random numbers click the red die icon or drop the Change menu and choose Simulate Again Note that the Hill slope changes Step 4 Simulate many data sets Start from the nonlinear regression results click Analyze and choose Monte Carlo simulation On the first Simulations tab choose how many simulations you want Prism to perform For this example enter 1000 On the second Parameters to tabulate tab choose which parameters you want to tabulate The choice is the list of analysis constants that Prism creates when it analyzes the data For this example we only want to tabulate the two confidence limits for the Hill Slope On the third Hits tab define a criterion which makes a given simulated results a hit For this example we ll define a hit to mean that the confidence interval brackets the true value of 0 5 set in the simulation So a hit is defined when the lower limit is less than or equal to 0 5 and the up
284. lcome dialog you can clone from any file project that is open from one you ve used recently or from projects you ve save as examples Portfolio 1995 2014 GraphPad Software Inc s GraphPad Prism User Guide Open an example Prism file containing a polished graph simple or complex Explore these portfolio graphs to learn how to get started with Prism and to learn some of its advanced features People who have already learned the basics of Prism will appreciate these portfolio files more than beginners 4 4 The five sections of a Prism project A Prism project can contain a lot more than a single graph or data table A Prism project file has five sections Each can contain up to 500 pages also called sheets a Data tables Enter and organize your data for analyses or graphs Learn more Info tables Keep a record of experimental details or of constants you want to use in analyses Learn more Constant Value Notes Expenment Date Agpr 25 2008 Enzyme actwity measured in Expenment if 20044 plasma fraction of blood withdrawn of 10 gu ertwbite f vehicle oily Notebook ID Gabde s lab 2007 Proect Conv Enz intebtor a eee ee Expenmenter Gabe Protocol See book CV 00905 pg 3 Results These sheets show the results of your analyses You can copy from here and paste parts of your results onto graphs Learn more 1995 2014 GraphPad Software Inc Getting started with Gra
285. ld not be useful when run from Prism it would be useful as a way to launch Prism For Windows Create a shortcut icon with a target something like this C program files GraphPad prism 6 prism exe doit pzc Double click that icon to launch Prism and run the script doit pzc For Mac You cannot create an icon that launches Prism running a certain script All you need to do with Prism Mac is double click on the script icon and that will launch Prism and run the script The script shown above instructs Prism to open a template today pzt and import today s data today txt presumably changing daily into the file and go to the graph Once you have set this up a few minutes and also have a mechanism so the data file is updated daily outside the scope of Prism you simply double click to see a new graph of today s data 23 1 6 Script example 5 Import data and info constants from the script file Script command Comments GoTo D 1 Go to the first data table InsertData 1 0 Insert data from the script file starting at row 1 column O the X column lt DATA gt Data block within script file 1 000 564 1452 Adjacent values are separated by tabs 2 000 389 7727 3 000 138 9337 1995 2014 GraphPad Software Inc ns GraphPad Prism User Guide 4 000 115 3119 lt DATA gt GoTo I 2 SetInfo Experiment 2 0 SetInfo 345 2 1 SetInfo Experimenter 3 SetInfo Dan Brown 3 1 Go to second info sheet Se
286. le The last two choices grand mean and median only appear if you choose a grouped column scatter graph This next example is set up to enter mean SD and N for each bar Y subcolumns for replicates or error bars Enter and plot a single Y value for each point O Enter 3 replicate values in side by side subcolumns Plot Mean with SD Enter and plot error values already calculated elsewhere avail Mean SEM N Mean ZEV N Two wa Mean amp SD Repeate Mean amp SEM Bonferrc Mean amp ZCV Organiza Mean Error Mean Upper Lower Limit CV is the coefficient of variation which is equals 100SD Mean If you enter the CV Prism will plot SD error bars If you enter N along with the SD SEM or CV you will be able to plot the SD SEM or 95 CI via choices on the Format Graph dialog If you omit N Prism can only plot the error value you entered 1995 2014 GraphPad Software Inc 152 GraphPad Prism User Guide Changing the subcolumn format To plot the replicates or error bars differently you don t have to remake a graph Instead click the Change graph type button Change L Li KON X ty n amp Use the Format Data Table dialog to specify how you will enter the replicates or error values If you change from entry of mean and SD to entry mean and SEM only the labels change not the numbers This lets you correct a mistake if you were actually entering SEM values but mistakenly set up t
287. le file that tabulates the logEC50 values along with the standard error and the R square of the fit Script command Comments SetPath c data june21 This sets the disk and directory to be used for the rest of the file OpenOutput results txt Create a file called results txt to contain the output Table Text Start a tab delimited text table in that file Open dr pzf Open the Prism file dr pzf ForEach dr txt Loop for all files that begin with dr have the extension txt and are located in the disk and directory defined by the SetPath command Goto D Go to the data section to the data table last visited ClearTable Erase all data from the table Import Import the file defined by the ForEach statement into the first empty columns WTable File name F Write the file name into the output file GoTo R 1 V2 Go to the second view of the first results page This is the table of nonlinear regression results For each file Prism will notice that the data have changed and will rerun the fit 1995 2014 GraphPad Software Inc Wtable logEC50 5 1 Write to the output table the value on the fifth row first Y column A and label that column of the table logEC50 WTable SE of logEC50 11 1 Write the SE of the logEC50 from the 11th row of results into the next column Wtable R2 21 1 Write the R2 value into the next column Next Loop back to the ForEach statement and read the next file
288. lick on the New button in the Sheet section of the Prism toolbar and choose New Data Table Graph Choose the kind of data table on the New Data Table dialog When you first go to look at the graph Prism will prompt you to choose what kind of graph you want it to create Create a new graph from existing data To create an additional graph from an existing table go to that table click the New button and choose New Graph of Existing Data Then choose the graph type Duplicate a graph and plot the same data To duplicate a graph go to it click the New button and choose Duplicate Current Sheet Prism will create a duplicate of the graph and both copies will plot the same data Now you can change the properties of the new duplicate graph without affecting the original Duplicate a graph and plot new data Prism offers two ways to duplicate a graph with its data table and analyses One approach is to go to the graph you want to duplicate click the New button and choose Duplicate Family The duplicated graph will look identical to the one you started with but it will be graphing a duplicated data table Edit the data on that table and only the new graph will update The second approach is to clone a graph Click the New button and choose New Data Table Graph On the New Data Table and Graph dialog choose the Clone tab and choose which graph to clone Use tabs at the top to clone from a current project a recent project or
289. linear equations This simplification means that the intervals can be too optimistic too narrow so your true confidence level may be less than 95 How can you know whether the intervals really do have 95 confidence There is no general way to answer this But for any particular situation you can get an answer using simulations This page explains how to do this with Prism using the Monte Carlo feature new to Prism 6 We will simulate a dose response curve and ask how accurate the 95 confidence intervals are for the Hill Slope Christopolous suggested that the distribution of HillSlope can be asymmetrical and suggested fitting the logarithm of the HillSlope instead 1 Step 1 Simulating the first experiment From anywhere click New Analysis and choose Simulate XY Data To follow this example exactly make these choices e X values tab Start at X 9 increment each X value by 0 5 and stop when X equals or exceeds 3 0 e Equation tab Choose the folder Dose response Stimulation and choose the equation log agonist vs response Variable slope e Parameter values tab Choose to simulate one data set with 3 replicate values Set Bottom 250 Top 5000 logEC50 6 and HillSlope 0 5 e Random error tab Random error is Gaussian absolute with SD 200 Step 2 Fit the first experiment 1 From the graph click Analyze and choose Nonlinear regression Or click the nonlinear regression shortcut button in the Analysis part of the too
290. log Format Graph j 3 as Appearance Data Sets on Graph Graph Settings Graph i e bee hee e Selected graph Staircase with ticks starting at 100 Show result as Fractions All pont Percents Censored por Connecting lines 1995 2014 GraphPad Software Inc 262 GraphPad Prism User Guide Choose the format of lines connecting data points for a survival plot Consider using arrows Show Area fill Choose to show area fills below or above the plot lines Click the All button to turn on this feature for all the data sets on a graph J Show area fill Filcoke Pattern Ee Patten color i Posibor Below x d o a o o al Percent survival 0 0 50 100 150 200 250 Days after randomization Plot on which Y axis Specify which axis to use for each data set If you choose to plot on the right Y axis Prism will create that axis if it doesn t already exist Legend Select Show legend to create a legend for this data set Prism automatically uses the column titles in your data table as legend labels You can also edit the labels in the legend Double click on the legend text and type whatever you like Use the Revert Legend to Column Titles button in the Legend section of the Format Graph dialog to change the labels back to match the column titles This button is only available if you have edited a legend 14 4 2 Changing the plotting order of data sets How
291. loop a certain number of times for simulations over all matching files repeated importing or over all sheets in a section to print or export End the loop with a Next statement You cannot nest loops Starting and ending the loop There are three ways to start a loop e Loop a specified number of times example ForEach 100 e Loop over a set of files example ForEach CSV e Loop over all sheets in the current section ForEachSheet For all three kinds of loops the Next statement ends the loop Variables in loops The Prism scripting language lets you use these four variables in any command that exports text e F The name of the file This is useful in ForEach loops that import a set of files F is the file name before the period e X The file extension without the preceding period e S The name of the current sheet This is useful when looping over all sheets in a file e N The loop number This is useful in simulations which loop a set number of times These variables can be preceded and or followed by other text They can only 1995 2014 GraphPad Software Inc be used within a script loop Regenerate random numbers One common use of a Prism script is to do Monte Carlo analyses First create a Prism file that uses the analysis Simulate data with random scatter to generate data and links those simulated data to another analysis say a nonlinear regression Inside each loop use the Go
292. m AppleScript Here is a sample AppleScript that launches Prism and tells it to run the script named DR2 located in the P4scripts folder on a disk named HD tell application HD Applications Prism4 Folder Prism activate open file HD P4scripts DR2 pzc end tell 1995 2014 GraphPad Software Inc 23 3 3 Launching a Prism script from outside Prism Windows One way to launch a script is from within Prism drop the File menu and choose Run Script You can also launch a Prism script from outside Prism When you launch Prism this way if the script closes all open Prism files then Prism will shut down when the script ends Otherwise Prism will remain open Launching a Prism script from a desktop icon To create an icon that launches a Prism script point your mouse to an empty spot on the desktop click the right mouse button and select New Shortcut Enter a command line that starts Prism and points to the Prism script file to launch Include the symbol in front of the path to the script name If either path includes spaces include the entire path in quotes as shown below C PRISM5 PRISM EXE C PROGRAM FILES PRISM 6 SCRIPTS DOIT PZC Shelling to Prism from another program To shell simply means to launch one program from another Here is an example of a shell command in an Excel VBA macro Shell C prism 5 prism exe C prism 6 dr2 pzc The shell command has to specify both the full location of prism exe and
293. m NUMDELSS ccceeeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeseneeeeeneeneees 343 Transforming normalizing etc 345 1995 2014 GraphPad Software Inc 1 Key concept Manipulating data ce cccccceeeee eee eeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeneeeeeeeeeneeeeneennane 347 2 Transform datas ciiiccicscvecsisccvectecccecveteceveviectecesete covectedceeeueteceveenscdevveneecevesiedecenvedecevevencceeeeey 348 3 R move baseline sariini aaan EEE SA EE AEAEE TAAT Aai 351 A gt NormaliZe sr seeetce sect see tieue irena aa Aa aaae eaaa aana aaa ana EEE aaa aaa aaae aaa 353 5 Transpose rows and ColUMNnS s ssssssssssssnurrnnnnnnnnnnnnnnnnnunnnnnnnnnnnnnnnnnnnnnnnnnnnn nanus nennen nn nnna 355 6 Prune POW Serioa De ceca aa ea aae a aa e aaa vues a a a aaa eaae aia 356 7 Fraction Of Total cisccciicsiccccccsecesescceveceesctevecsceeeedccceeseeec stewed scctened seeeeensecteeeveseteeeivenetenedasneneds 357 Part XIX Page layouts 357 1 Creating layouts wccciciiciccticcccceicicceseticcesteeecineeeeeeteeeeeaentee ded enteewed etuina veiin iatna iu ia aeaiiai 359 2 Choosing the initial arrangement cccecececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseaeeeeeeeeeeeeseaeeeeeesaneeeees 360 3 Assigning a graph to a placeholder cceccceeeceeeeeeeeeeeeeeeeeeeeeeseeeeeeeeeeeeeseneeeeeeeeeseeneeneneees 362 4 Adding another graph to the layOut cccceeeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeneesaeeeeneeenes 363 5 The size of graphs on l
294. m User Guide e Object linking and embedding This means you can paste a Prism graph into another program and double click to edit in Prism e Excel linking and embedding This means you can paste Excel data into Prism and double click to edit within Excel e Audio notes can be embedded on graphs or layouts e Import and export EMF and WMF images e Send to Word with a single click e One click to post a graph or layout on a web site e High contrast printing with no grays and no colors e Visual Basic for Applications VBA commands to launch Prism and start a script e Export in the older PCX format Features in Mac but not Windows e Spell checking of text anywhere in the project e Quick Look Lets you preview graphs within Finder Leopard and later only e Color eyedropper While setting any color click the magnifying glass tool then click on any color on any window to select that color e Send to keynote with a single click e Use an Automator action to launch Prism and run a Prism Script e Export in PICT format File compatibility Files saved on one platform can be opened on the other In almost all respects this just works and you don t have to think about it But there are three exceptions e If you use Prism Mac and copy a graph from one project and paste it onto a 1995 2014 GraphPad Software Inc How Prism is unique 4 layout on another project Prism can handle this in two ways By default it
295. m often make the mistake of thinking that each Prism file can only have one data table and one graph Not so Each file can contain up to 500 data tables info sheets analysis results graphs and page layouts Prism lets you open more than file at a time While working with Prism you can open multiple Prism files The details are Slightly different for Windows and Mac Prism Windows Multiple open projects in one overall Prism window There are two ways to work on a second Prism project If you use the File New or File OQpen commands or the corresponding toolbar buttons you ll open a second project within the overall Prism window You can then open or create a third fourth project All are contained within a master parent Prism window This means that even if you use two or more displays all these projects must be shown on one computer display All open projects share the same toolbar Use the Windows menu to move from one project to another Use the Navigator or bottom toolbar to move between sheets in one project file Prism Windows Two open projects in distinct Prism windows 1995 2014 GraphPad Software Inc Getting around in Prism 7 If you want to open a second Prism window simply launch Prism again To do so you must double click on the program icon Double clicking on a Prism file when Prism is running will always open that file in the instance of Prism already running To launch a second instance of Pr
296. m values from a Gaussian distribution using routines adapted from ideas presented in Numerical Recipes in C W H Press et al second edition Cambridge Press 1992 The function RAN3 defined in Numerical Recipes generates uniformly distributed random numbers and the function GASDEV transforms them to a Gaussian distribution with a mean of zero and a standard deviation you enter If you choose relative error Prism first calculates a random number from a Gaussian distribution with a mean of zero and with a SD equal to the percent 1995 2014 GraphPad Software Inc sa GraphPad Prism User Guide error you enter It then multiplies that percentage times the ideal Y value to yield the actual random value that is added to the Y value Prism also can generate random numbers from a t distribution with any number of degrees of freedom df This lets you simulate wider scatter than Gaussian If df is low this distribution is very wide If df is high more than 20 or so it is almost indistinguishable from a Gaussian distribution If df 1 the distribution is extremely wide lots of outliers and is identical to a Lorentzian distribution also known as the Cauchy distribution Prism uses this equation to generate random numbers from the t distribution with df degrees of freedom In this equation Rand is a random number drawn from a Gaussian distribution with mean 0 and SD 1 To compute a random number from a t distribution with df degre
297. m with Mac 404 Vertical vs horizontal graphs 203 View importing option 174 View toolbars 75 Viewing Prism files 106 W Walker Jimmy 467 Wand wizard to analyze data 96 WCell command 433 WCol command 433 WDate command 433 Web publishing 405 Welcome dialog 53 whiskers 237 Widths of columns 137 Windows differences OLE 399 Windows menu 76 Windows vs Mac compatibility 102 Windows vs Mac differences 43 WMF or EMF format 399 WMF exporting 384 WMF importing 376 Word 399 Word sending to 89 Word using to add formatted text 374 Word One click export to 397 Working with multiple projects 105 Working with multiple sheets 81 Working with sheets 80 Working with text filles 168 WRow command 433 WSheet command 433 WTable command 432 WTCol command 433 WText command 433 WTitle command 433 WTSheet command 433 X Xand Y transposing 355 X values regular sequence 143 XLS files importing 169 XML 100 XY datatables 113 1995 2014 GraphPad Software Inc Index 477 _Y Y axis adding one on right 284 Yellow highlighter 88 oF Zooming 74 379 1995 2014 GraphPad Software Inc
298. mbols or bars plotting those data Use Prism Magic to make graphs consistent Select one or several graphs click the Magic Make Graphs Consistent button choose an example graph and all your graphs will be changed at once Change fii E hi A Au uty amp Change colors by picking a color scheme Rather than change colors of every graph element separately use color schemes You can use ones we provide or create your own Change Gi LS Li KON K ud nie Prism can plot error bars directly from raw data Prism can plot error bars directly from raw data Prism lets you enter SD or SEM if 1995 2014 GraphPad Software Inc GraphPad Prism User Guide you have calculated them elsewhere but there is no need to do so Enter your raw data and let Prism do the rest Prism offers analyses that perform row and column descriptive statistics but these are only to help you understand the data You do not need to run these analyses to plot error bars To add data to a graph drag a table from the Navigator and drop onto the graph After you drop the data or results table onto the graph a dialog will pop up where you can choose which data sets to include and which axis to plot those data on right or left Data analysis tips Don t run the analysis again change the analysis choices If you made a mistake or want to try different analysis choices you can always return to the analysis parameter dialogs Don t repeat t
299. ment Info amp Notes Row1 87 Row2 23 Row3 45 Row4 54 Goto Source Use these settings as the defauk foe Import and Paste Special Restore orignal def art Help Cancel Paste Once you ve pasted linked data into a Prism data table click Open File to open and edit the data file If it is an Excel file you ll open Excel If it is a text file you will open a text editor 1995 2014 GraphPad Software Inc Importing and exporting data 175 12 8 3 Filter tab Choices on the Filter tab of the Import and Paste Special dialog let you choose which portions of the data file to import m Import and Paste Special Choices me Source View Fiter Placement Info amp Notes Unknown and excluded values Missing values are denoted by fie 39 of na V Exclude values preceded or followed by asterisks fie 45 6 or 45 6 Rows Start at Row 1 Enda Last Row Row Skip al rows until column 8 Skip al rows after column Skip every row where column 8 Decmate Import a row skip rows import another row and repeat Cokunns Start at Column 1 End at Last Column Column Unstack Column 4 contains data Column contains group number Skip columns Import a column skip cokmnis mpat another column and repeat Use these settings as the defauk foe Import and Paste Special Restore ongnal default Help Cancel Paste Unknown and excluded values When entering data you can leave any parts of
300. mple to learn the details Simulations tab How many simulations How many simulations should you run If you make only a few simulations the 1995 2014 GraphPad Software Inc 33 GraphPad Prism User Guide results will be affected too much by chance Running more simulations will give you more precise results but you ll have to wait longer for the calculations to repeat When just playing around it might make sense to use as few as 100 simulations so you can see the results instantly When trying to polish simulation results it can make sense to use as many as 10 000 or 100 000 simulations A good compromise is 1000 Append If you go back to run more simulations check an option box to append the new simulations to the existing results rather than start fresh Random seed The choice of random numbers used in a series of simulations depends on the random number seed used to generate the first set of results By default Prism picks this seed automatically based on the time of day and presents this seed in a floating note superimposed on Monte Carlo results If you want two or more Monte Carlo analyses to use precisely the same data sets SO you can compare two ways of analyzing those data enter that random seed on the Simulation tab Parameters to tabulate tab Prism lists all of the analysis constants generated by the analysis Check the ones whose values you want to tabulate You cannot change the set of valu
301. multiple comparisons Prism 6 has a new analysis to perform one t test per row of a data table with replicates placed side by side It corrects for multiple comparisons either by using either a more stringent definition of statistical significance or controlling the False Discovery Rate FDR You can also choose not to correct for multiple comparisons e More graphing choices Prism 6 offers options to automatically graph ranks of nonparametric tests and differences for paired t test and repeated measures ANOVA e Browne and Forsythe test To test equality of variances in one way ANOVA Prism 6 computes both the Browne and Forsythe test as well as the Bartlett test which previous versions computed e Method of Pratt There are two ways to compute the Wilcoxon matched pairs test when some of the pairs are identical so the difference is zero Prism 6 offers both choices The new choice is the method of Pratt for tied rows Simulations and Monte Carlo analyses Simulations can be useful even when you just simulate one data set and view 1995 2014 GraphPad Software Inc What s new in Prism 6 the graph and analysis Prism 5 let you simulate XY data Prism 6 now let s you also simulate column data and 2x2 contingency tables For XY and Column data Prism 6 can include not only Gaussian random scatter but also scatter computed from a Poisson or binomial distribution Simulations are even more useful when you repeat the simulation
302. n Prism Prism 6 makes these more obvious on the Welcome dialog so more people will try them 2 6 What s new Data tables e More columns Prism 6 allows you to enter data in up to 256 data set columns Prism 5 allowed only 104 1995 2014 GraphPad Software Inc z GraphPad Prism User Guide e More subcolumns When creating an XY or grouped table Prism 6 allows up to 256 subcolumns per data set compared to only 52 subcolumns with Prism 5 This lets Prism compute repeated measures two way ANOVA with more subjects e Paste link data or results from Prism You ve probably encountered situations where you need to copy values from a results table and then paste onto a data table perhaps using options in the Paste Special dialog to transpose or rearrange the values Prism 5 could paste the values but there was no link so it was not possible to trace where the values were pasted from and the pasted values did not update when the original data were edited or replaced Prism 6 lets you paste link so values pasted onto the data table are linked to their source and will automatically update e Reformat a select set of points Select any block of data in a data table right click and choose Format Points to change the color or size or shape used to graph that subset of points e Long column titles With Prism 6 the length of column titles has no real limit Prism 5 limited the length of column titles and many people bumped i
303. n a graph You can copy any part of a results table and paste it onto a Prism graph or layout The link will be live so will be updated if you edit the data or change the analysis parameters Unpaired t test data 100 YTitle Unpaired t test a P value P value summary Are means signif different P lt 0 05 One or two tailed P value t5199 N i Double click on the embedded table to bring up a dialog that will let you adjust its font borders etc 1995 2014 GraphPad Software Inc 326 GraphPad Prism User Guide When you copy a single cell of a table you have two choices when pasting e Paste as text First use Prism s Text tool to create a text box then paste a results sheet value into it In this case the value you copied will be pasted as text with no link back to the analysis T T 500 Specific Binding fmol mg N aw Q Q Q o o o gt Q o o 0 25 50 75 100 125 150 Concentration 1I ICYP pM e Paste as link If you paste directly onto the graph or layout not while entering text you will paste an embedded table with one cell that will automatically update when the results are recomputed 16 8 Hooking to analysis and info constants What is hooking Prism lets you hook the results of some analyses into the parameters dialog of other analyses and graphing dialogs The value you hooked is then used in that analysis or graphing choic
304. n an argument is in lower case it describes the value you will enter When an optional argument is in uppercase you enter that exact word if you want that option General commands Adding comments to a script Loops and simulations Creating new sheets Changing data tables Changing graphs Setting the default drive and folder Opening and saving Prism Files Importing data Changing info constants Including data and info constants in the script file Exporting a graph or layout Exporting data results or info tables Copy and paste Writing to Prism text HTML XML or SQL tables Writing to text files Send to Microsoft Office Special purpose commands 1995 2014 GraphPad Software Inc 420 GraphPad Prism User Guide 23 2 1 Navigating a project Commands GoTo lt section D I R G or L gt lt sheet gt lt view gt GoTo Explanation The GoTo command is used in almost every script to navigate to a different sheet in the project as these examples show Example GoTo G GoTo 3 GoTo G 3 GoTo V2 GoTo R 3 V2 GoTo GoTo Notes Description Go to the graphs section to the most recently viewed graph Go to the third sheet of the current section Go to the third graph Go to the second view subpage of the current results Go to the second view of the third results sheet Go to the next sheet in the current section Go to the previous sheet in the current
305. n experimental intervention was performed A B op te oe ety 0 1 2 3 4 e Faster graphing Regenerating graphs with tens or hundreds of thousands of points can be slow If you are impatient Prism 6 lets you specify that a graph only show one out of every K points you specify K to speed up graphing on screen It also lets you work on the graph move things around add text or drawings change axis properties etc as the data points are plotted on screen e Create a graphs with only a right Y axis Prism has always made it easy to add a right Y axis as a second axis But it has been difficult to create a graph witha single Y axis positioned on the right side To do this with Prism 5 can requires positioning the left only Y axis in on the right side of the graph and then assigning data sets to the left axis even though it is on the right side of the graph Confusing Prism 6 makes this more straightforward Turn off the left Y axis and create a right Y axis to which you assign data sets 1995 2014 GraphPad Software Inc GraphPad Prism User Guide e More subcolumns Prism 6 allows up to 256 subcolumns for replicates Prism 5 allowed only 52 2 11 What s new Grouped graphs e Draw lines between groups Wild type Knock out G m S we p e More easily create grouped low high box whiskers and scatter graphs Change Graph Type Graph family Grouped X Plot individual values Plot summar
306. n indexed data file you may want to import only the data in column 2 and use the values in column 3 to define the two groups Row Col 1 Col 2 Col 3 1 12 123 5 2 14 142 6 3 13 152 5 4 12 116 6 5 11 125 6 6 15 134 5 Check the box to unstack data only from column 2 using column 3 to identify the 1995 2014 GraphPad Software Inc Importing and exporting data 177 groups Prism will automatically rearrange the data so they look this like Row First Col Second Col 1 123 142 2 152 116 3 134 125 The column that identifies the groups must contain integers The lowest integer defines the group whose values will be placed in the column containing the insertion point in Prism If there are gaps in group numbers Prism will leave blank columns If you use Paste Special to paste data from the clipboard _ the column numbers in the Filter tab are relative to the ES range of data you copied to the clipboard For example if nci you copied cells C13 F45 from Excel to the clipboard then column 1 in Prism s Filter tab refers to the data in Column C in Excel the first column of the copied range 12 8 4 Placement tab The Placement tab of the Import and Paste Special dialog lets you rearrange your data as you import paste into Prism 1995 2014 GraphPad Software Inc GraphPad Prism User Guide g Import and Paste Special Choices r Source View Fiter Placement Info amp Notes Names Rename data table u
307. n nnne 408 Printing data and results tableS ssssssessnusnuunnunnnunnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn nnmnnn 408 Printing raphs and layouts 2 cccceccrocsieeehekeciieecsivccccasccesvecstvecstadecedendcevccdshadesavecsseesdhete 409 Printing the gallery iecscociicec ce ccesecteives oie aaea aaa aaraa a a aa a AE en aaia a raae 410 Scripts 411 Exam ple seripts E E A a A A T 413 Key concept What is a Prism script ccsscceeseeeseeeeseeeeeeeeeeneeeeeaeeeeaneesaeeseaeessaeeeeaeeeseaeeeeaeeeseeeneneeesaees 413 Script example 1 Repeatedly im port data cceecccesceeseeeeseceeeeeeeeeeeseaeeeeaeeesaeeeeeeeesaeeeseeeeseseesaeeeseeeseeeeees 414 Script example 2 Monte Carlo analysis cs cccssceeeeeeeeeeeeeeeeeesneeeeeeeeeaeeesaeeessaeeesaeeesaeeesaaseeeaseeseeeseeneeas 415 Script example 3 Import several files Onto one table ceeeceseeeeeeeeeeeeeeeeeeeeeeeeeseeeeseeeeeeeeeesaeeeseeeeeeeeeeees 416 Script example 4 Open a template and import data ccccsseeseeeeeeceeeeeeeeeeeseeeeeseeeeseeeeseeeesaeeeseeeeeeeeeeeas 416 Script example 5 Import data and info constants from the script file ceecceeeeeeeeeeeeeeeeeeeeeeeeeeeeee 417 Script example 6 Import data into Several tables ccsecccesseeeeeeeeeeceeseeeeseeeeseeeesaeeeseeeesaeeeesaeeeseeeeeeeeeeeas 418 Script synta xis soo sesasics oo ka Psed pea sec See a eed acd vedas tena sncdee chews pe Aana vie ben
308. nc Distinguishing the six kinds of data tables Table format na cll Uh Survival Standard Experimental a i 7 Each row represents a distinct subject You can optionally use row titles to identify the subjects Each column represents a treatment Enter elapsed time usually in days as X Prism does not let you enter dates For each subject enter a code for Y Enter 1 for a subject if the event death occurred at the time entered into X Enter 0 if the data are censored Data are censored when you simply dont know what happened to the subject after that time or do know but can t use the information For a more complete discussion of entering survival data and interpreting the results see How To Survival Analysis Error bars When Prism plots a survival curve it can include SE or 95 CI error bars These are computed as part of the Kaplan Meier method for creating the Survival curve You can t enter error values directly they are computed from all the data 9 8 Parts of whole tables A Parts of whole table is used when it makes sense to ask What fraction of the total is each value This table is often used to make a pie chart 1995 2014 GraphPad Software Inc 120 GraphPad Prism User Guide Analyses performed on parts of whole data e Fraction of total e Chi square goodness of fit Example of a Parts of whole table The example below shows the number of students who received gra
309. nce of symbols bars etc Choose which properties of your example graph you wish to apply fonts colors axis range and more and preview your changes poems Remember you don t have to change your graphs one at a time Select many graphs and use Magic to create a uniform look 1995 2014 GraphPad Software Inc What s new in Prism 6 amp Recently used User defined equations amp Dose response Stimulation loglagonist vs response Variable slope loglagonist vs normalized response loglagonist vs normalized response Variable slope Dose response Inhibition amp Dose response Special amp Binding Saturation Binding Competitive Binding Kinetics _ amp Enzyme kinetics Exponential Lines Polynomial amp Gaussian B Sine waves FX is not already the log of dose go back and transform your sata The curve wil have a standard slope Hil Slope 1 0 Af ary basal response has been subtracted consider constraining Bottom to a constant value of 0 0 loglagorust vs response Q Leam about this equation Fitting method Least squares ordinary ft Robust fit Automatic outlier elimination interpolate C Interpolate unknowns from standard cury Confidence intervak None 3 How Prism is unique GraphPad Prism is very different than other scientific 1995 2014 GraphPad Software Inc 3 GraphPad Prism User Guide graphing programs As you start to use Pr
310. ndscape vs portrait Tables 408 Launching scripts Excel 445 Launching scripts from outside of Prism 443 Launching scripts using MacScript Automator or AppleScript 441 Launching two instances 76 Layout arrangement 360 Layout legends 369 Layout tooltips 70 Layout adding anther graph 363 Layouts 362 Layouts creating 359 Layouts exporting 397 Layouts exporting to file 384 Learning Prism 10 Left panel navigator 68 Legends 369 License agreement 462 Limits of axis 279 Lines 375 Link 399 Linkback 404 Linked analyses 71 Linking and embedding data 160 Linking and embedding data objects 172 Locking a sheet 84 Locking a table freezing 322 Locking in position 379 Log axes 307 Log transform 348 Mac differences no OLE 399 Mac differences pasting Prism graphs 404 Mac vs Windows compatibility 102 Mac vs Windows differences 43 Macros scripts 419 1995 2014 GraphPad Software Inc Macros Prism scripts 413 MacScript 441 Magic Make graphs consistent 197 Magnifier 74 Major ticks 283 Make Graphs Consistent 197 Managing sheets 80 Master legends 369 Merging 105 Method file 96 Method vs template 98 Methods applying 96 Methods savinginalab 451 Microsoft Equation Editor 376 Microsoft Excel files importing 169 Microsoft Excel pasting data from Mac 165 Microsoft Excel pasting data from Windows 163 Microsoft Office 399 Microsoft Office sending to 89 Minor ticks 283 Missing toolba
311. nes cause Prism to exit and free the memory used by the Prism object There are two advantages to using OLE automation rather than the Shell statement First with OLE automation Visual Basic and Prism run sequentially with no possibility of Visual Basic trying to obtain results that haven t been created yet Second with OLE automation your Visual Basic program can direct Prism to import data from a particular folder Prism SetPath command without changing the Prism script Launching a script from an intranet web page Windows You can launch Prism from a link on an intranet web site First create a batch file on your web server that calls using the Call command the program and individual configuration files For example create a file called StartPrism bat containing a single line something like this Call N Program Files PRISM5 PRISM EXE OC WINDOWS prism5 cnf Or this Call F Prism Prism exe F PRISM PRISMSCRIPTS DOIT PZC Of course you ll need to adjust this example depending on where you have installed Prism The drive letters are aliases for the server drive In the first example the first part opens Prism and the second part tells Prism where to find the configuration file In the second example the second part launches a Prism script Next edit your web page to include a hyperlink to the batch file For example HTML link the text Prism to the file StartPrism bat 23 3 4 Using Prism scripts with Excel E
312. nless enforcement is prohibited by applicable law and then only to the extent prohibited by applicable law the following actions are expressly prohibited a You may not and may not permit any third party to decompile disassemble or reverse engineer the Software b You may not modify translate adapt arrange or create derivative works of the Software or the User Documentation 1995 2014 GraphPad Software Inc Support and license 465 c You may not sell transfer rent lease loan or otherwise distribute all or any portion of the Software the User Documentation or any other rights granted to you in this Agreement d Except as otherwise expressly provided in this Agreement you may not allow access to the Software or the User Documentation over the Internet including without limitation in connection with a web hosting commercial time sharing service bureau or similar service e You may not remove alter or obscure any copyright or other proprietary notices labels or marks from the Software or the User Documentation f You may not otherwise install access or otherwise use or copy the Software or the User Documentation other than in strict compliance with the terms of this Agreement g You may not use the Software in medical diagnosis or treatment or in applications or systems where the Software s failure to perform can reasonably be expected to result in significant physical injury property damage o
313. nonlinear regression you can choose to express the parameters in multiple ways For example choose between fitting a rate constant or a half life Hougaard s measure of skewness can help you choose the parameterization where the uncertainty is closer to symmetrical so the confidence intervals will be more accurate e Adjusted R2 Prism reports the adjusted R which takes into account the number of degrees of freedom and so can be compared between models with different numbers of parameters Linear regression e Convert from linear to nonlinear regression with one click Linear regression can be viewed a special case of nonlinear regression Prism s nonlinear regression analysis can be used to fit a straight line and there are more than a dozen reasons why you might want to do so But few people think of using the nonlinear regression analysis to fit a straight line Prism 6 makes it easier to switch simply click the More choices button on the linear regression dialog e Copy the linear regression equation Prism always reported the best fit values for the slope and intercept but not in the form of an equation Prism 6 now reports the equation for the line ready to copy and paste onto a graph or into a manuscript 1995 2014 GraphPad Software Inc What s new in Prism 6 21 A Control Y B Treated Y Linear reg 1 Best fit values 2 Slope Y intercept when X 0 0 Xintarcgi vige i ge v
314. not expire You may install the viewer on any number of computers The Viewer lets you view existing Prism files but does not let you create new files or edit existing ones YOU ARE NOT PERMITTED TO BYPASS OR CIRCUMVENT THESE LIMITATIONS USE OF PRIOR VERSIONS IF YOU UPGRADED If you purchased your license as an 1995 2014 GraphPad Software Inc 464 GraphPad Prism User Guide upgrade from a prior version you may run the prior version on the same computer you installed the Software You may not transfer your license for the prior version to another computer or to anyone else INSTALLATION AND USAGE You may install and use the Software on up to the Authorized Number of Computers THIS IS NOT A CONCURRENT USER LICENSE The Authorized Number of Computers includes each Computer that at any time is or has been given access to the Software regardless of whether such Computer is running the Software at a particular point in time AUDITS To ensure compliance with this Agreement you agree that upon reasonable notice GraphPad or GraphPad s authorized representative shall have the right to inspect and audit your use of the Software Any such inspection or audit shall be conducted during regular business hours at your facilities or electronically either by GraphPad or by representatives authorized by GraphPad for this purpose If such inspections or audits disclose that you have installed or permitted access to the Software in a manner that
315. ns on the Change toolbar To link a global Info sheet to a specific data table Click this button in the Change toolbar to bring up a dialog to select which data table the Info Sheet is linked to a E Change To change which info constants appear by default on new Info sheets Use the Info Sheet tab of the Preferences dialog You can also choose whether or not Prism will automatically create a linked Info sheet to accompany every new data table you create To import info constants into an Info sheet at the same time you import data See here for the details To hook info constants into an analysis or graphing dialog You can hook Info sheet constants as constraints in nonlinear regression or as constants when transforming You can also Hook to Info sheet constants to create custom ticks set axis limits etc You ll know when it s possible to insert hook an info constant because you ll see the fishhook icon next to the number entry field When you see this button in a dialog click on it to bring up a list of all Info and Analysis constants that can be hooked To insert a text file into the notes portion of an Info sheet Drop the File menu and choose Import 1995 2014 GraphPad Software Inc Organizing Prism projects 6 5 Annotating your work with floating and audio notes Floating notes Floating notes will show on the sheet but not when a sheet is printed or exported or copied to another ap
316. nt Choose whether you want each tick in line with or across from the regular ticks 1995 2014 GraphPad Software Inc 204 GraphPad Prism User Guide ALX 13 F gt Y Show Text Text line 1 Text line 2 Location Above ss B 0 1 2 3 4 You also can Hook the text of the label to an analysis or Info Sheet constant To add a fill between additional ticks or grid lines Check the option to fill between two ticks and choose the fill color and pattern 40 Mitotic Index e 0 6 00 09 00 12 00 1500 1800 21 00 24 00 0300 06 00 09 00 12 00 Time To create adjoining fills Prism can only fill the space between an Additional Grid line and one of its neighbors To create fills on both sides of a grid line place two additional grid lines at the same position and fill backward from one and forward from the other 1995 2014 GraphPad Software Inc Graphs Frame and axes 295 Mitotic Index Darkness 6 00 09 00 12 00 1600 18 00 21 00 2400 0300 06 00 09 00 12 00 Time To remove or change an additional tick Double click on the axis to bring up the Format Axes dialog Locate the tick you want to change in the Additional Ticks and Grid Lines section Details Le Click the Details button to open the Format Additional Ticks and Grid lines section and click on the Delete Tick button To create an additional tick or grid line by hooking an info or analysis constant The coord
317. nto that limit e Multiple line titles Each row or column title can now have two or more lines of text e Bold italics and underline You may also now bold italicize and underline text in row and column titles you could always use superscript subscripts and Greek e View all column titles at once A new tab in the Format Data Table dialog of Prism 6 lets you see and edit all the column titles This saves you from the scrolling back and forth to edit titles which was especially tedious with XY or Grouped tables with many subcolumns 2 7 What s new Working with other programs e LabsArchives Prism 6 integrates better with LabArchives As in Prism 5 click LabArchive it to upload files directly to LabArchives Now Prism also sends LabArchives a list of all words used in notes titles text boxes etc That mean you can search within LabArchives to find the file you need From the Welcome 1995 2014 GraphPad Software Inc What s new in Prism 6 25 dialog of Prism 6 you can open a file directly from LabArchives There is no longer a need to first go to labarchives com to download the file you want e Faster TIFF Exporting TIFF files at 1200 dpi from Prism Windows is much faster and more reliable doesn t lead to out of memory messages e Smaller TIFF Prism Windows can now compress TIFF files at 600 or 1200 dpi and compress even when you choose the CMYK color model not allowed in Prism 5 Windows e More export
318. o can perform repeated measures two way ANVOA with up to 256 subjects per treatment e The Greenhouse Geisser correction allows repeated measures one way ANOVA to work even when the assumption of sphericity is violated because the repeated measurements are made in too short a time interval so that random factors that cause a particular value to be high or low don t wash 1995 2014 GraphPad Software Inc What s new in Prism 6 15 away or dissipate before the next measurement In this case multiple comparisons are also computed so as to not assume sphericity Survival analylsis e Prism now computes the hazard ratio HR by two methods The logrank method and the Mantel Haenszel method e If people in group A die at twice the rate of people in group B HR 2 0 then people in group B die at half the rate of people in group A HR 0 5 Prism now reports the hazard ratio and its confidence interval both ways so you can report the one that makes most sense in your clinical context e If people in group A have a median survival time three times people in group B then people in group B have one third the median survival of people in group A Prism now reports the ratio of median survival times and its confidence interval both ways so you can choose which to report Analyses of column data t tests etc e Mann Whitney tests reports 95 CI of difference between medians The Mann Whitney test is often described as comparing the me
319. of ratios works much better 1995 2014 GraphPad Software Inc 16 GraphPad Prism User Guide e Kolmogorov Smirnov test Like the Mann Whitney MW test the Kolmogorov Smirnov KS test is a nonparametric method to compare two groups The KS test works by comparing the two cumulative frequency distributions and so has more power to detect subtle differences in the two distributions In contrast the MW test is better at detecting changes in the median The use of the KS test has become standard in some scientific fields Don t confuse this test with the the other version of the KS test used for normality testing e Faster nonparametric tests To avoid slow calculations Prism reports an approximate P value for nonparametric tests with large data sets Prism 5 also reported approximate P values when several values were identical and so tied for the same rank Prism 6 performs the exact calculations much faster hundreds of times faster and so does exact calculations even for fairly large data sets and even when several values are identical and so tie for the same rank e Identify outliers One of our free QuickCalc web calculators identifies outliers from a stack of values using Grubbs method Because this is one of our most popular calculators we created a new analysis in Prism 6 to identify outliers in a column of data e Perform many t tests simultaneously Computing multiple t tests can be useful so long as you correct for
320. olumn and column 1 is the first Y column If you have an XY table then column 1 contains the row titles 23 2 12 Copy and paste Commands Copy Copy rows columns first row first col lt first subcol gt 1995 2014 GraphPad Software Inc Paste first row first col lt first subcol gt Paste Explanation From a data info or results table copy selected values to the clipboard If you use the Copy command with nothing else Prism copies the entire sheet to the clipboard You can also specify which range to copy Note that columns includes subcolumns So if you want to paste triplicate values into two adjacent columns you need to enter columns as 6 or 7 if you also paste an X column If you use the Paste command with no arguments Prism will paste the entire table starting at the current position of the insertion point Copy and paste use the Windows or Mac system clipboard so will overwrite any other information copied to the clipboard 23 2 13 Changing info constants Commands SetInfo value rownumber lt position 0 name or 1 value or 2 notes gt SetValueToInfo infotable inforow datarow datacol lt datasubcol gt Explanation The SetInfo and SetValueToInfo commands inserts or changes a value into an Info sheet With the SetInfo command set position to O to change the name of the constant 1 to change its value the default choice or 2 to append to the notes in which ca
321. om color boxes at the lower left and wil stay there A few notes about this dialog e Choose a color shown on the left half of the dialog and you are done e The checkbox Use these custom colors in new projects only applies to custom colors you choose after you checked that option It won t apply to colors you chose before checking the option e When choosing a color by pointing at it on the right half of the dialog note that there are two choices The big box shows lots of different colors The smaller vertical slider to the right the upper right of the dialog is where you choose the shade of the color basically how much black is added This will default with the slider all the way down to maximum blackness In this position all the colors look black You ll need to move that slider up e With Windows it is not possible to choose a color by entering CMYK values But all colors can also be encoded as RGB 13 10 Rotating flipping reversing Change fi LE A at We The Rotate Flip button in the Change section of the Prism toolbar drops a menu with three choices You can reverse the order of data sets on a graph flip the page settings between landscape or portrait orientation or rotate column graphs from vertical to 1995 2014 GraphPad Software Inc 204 GraphPad Prism User Guide horizontal Reverse order of data sets For XY and Survival graphs this reverses the front to back order of data sets This only matters wh
322. ome the upper left corner of the pasted data 1995 2014 GraphPad Software Inc 166 GraphPad Prism User Guide Then click on the Paste amp or Paste Special rl button in the Clipboard toolbar ES View Insert Change Arr Cut Ctrl x Copy Crl c Paste Ccrlv Paste Transpose Ctr Shift T Paste Special CtrShift V TRE Peat aA PA tee a 00 a wf te AAP a Pee oe e Paste You will only paste the values that have been copied to the clipboard e Paste Transpose Converts data in Excel rows into columns in Prism and vice versa e Paste Special You ll then see the Import and Paste Special dialog where you can choose whether to filter and rearrange the data such as transposing Note that it is not possible to Paste Embed or Paste Link to Excel files on the Macintosh Those features only work on Windows Pasting an Excel table as a picture You can copy a portion of an Excel spreadsheet and paste it onto a Prism graph or layout This pastes a picture only and Prism cannot analyze or graph the values since the values are not in any Prism data tables 1995 2014 GraphPad Software Inc Importing and exporting data 167 Optical Density Units 00 01 02 03 04 OF Protein mg mL Importing Excel files Prism Mac cannot import Excel files Either copy and paste or save from Excel in CSV format and import that text file into Prism 12 5 Options when pasting data from Excel win or mac What Excel puts
323. ommands can not make other changes to the data table or number decimal format The DeleteAllDataSets command deletes all data and all links to analyses and graphs The ClearTable command erases all data to the left and below of the designated cell but maintains links to analyses and graphs 23 2 7 Changing graphs Commands ApplyColorScheme scheme name SetAxisTitle which axis X Y or Y2 new title SetGraphTitle new title SetAxisLimits which axis X Y or Y2 lt segment gt Top Bottom Interval value Explanation You must create graphs manually or by duplicating You can t change most graph properties via scripts but you can apply a color scheme change the limits of an axis and change the graph or axis titles When entering the graph or axis title you can only enter plain text and Prism does not provide tools to enter Greek letters math symbols superscripts or subscripts But note that Windows lets you enter some special characters by 1995 2014 GraphPad Software Inc holding Alt and typing its four digit code For example alt 0181 enters the Greek letter mu Each use of the SetAxisLimits command lets you change the range minimum and maximum values or interval of an axis Each use of the command only lets you change one of those values If you want to change the Y axis left Y so it ranges from 100 to 200 with an interval of 10 you need to use this command three times in any order
324. omputer and then move the files to the 1995 2014 GraphPad Software Inc a2 GraphPad Prism User Guide other computers you manage To do that you need to know where the files are stored Templates Templates are complete Prism files that you ll see listed on the Open File tab of the Welcome dialog You can tell Prism where to save templates in the File Locations tab of the Preferences dialog The default locations are listed below Prism Windows XP saves templates in system disk Documents and Settings All Users Application Data GraphPad On Vista or Windows 7 Prism saves templates in system disk ProgramData GraphPad Software Prism 6 0 Templates templat Prism Mac saves these files in Library Application Support GraphPad Prism 6 Templates templates categor Methods A method file contains a data table and linked analyses and graphs When you apply a method using the Wand Wizard to Analyze Data those analyses and graphs are attached to a new data table Prism Windows XP saves methods in system disk Documents and Settings All Users Application Data GraphPad On Vista or Windows 7 Prism saves methods in system disk ProgramData GraphPad Software Prism 6 0 Methods methods ca Prism Mac saves these files in Library Application Support GraphPad Prism 6 Methods methods category fo Examples An example file is a Prism graph with linked data and analyses You clone an example from the
325. on is to export from Prism as a pdf file and view that This works because eps and pdf files contain mostly the same information with a different Wrapper 21 5 RGB vs CMYK color models The Export dialog requires you to choose between RGB and CMYK color models when you choose to export a graph or layout in the PDF EPS or TIF format RGB Red Green Blue is based on projecting Red light plus Green light plus Blue light all projected together create white Black is encoded as the absence of any color Colors encoded as RGB are sometimes called spot colors CMYK Cyan Magenta Yellow black is based on ink Superimpose Cyan ink plus Magenta ink plus Yellow ink and you get black White is encoded by the absence of any color Colors encoded as CMYK are sometimes called process colors Even though it uses one more number to encode a color the CMYK scheme actually encodes a smaller color space than does RGB That means that the appearance of some colors will change when converted from RGB to CMYK Most noticeably bright colors in RGB left side of figure below will look duller and darker in CMYK as shown in the right side of the figure below from here 1995 2014 GraphPad Software Inc 392 GraphPad Prism User Guide 21 6 What you What will be printed in CMYK see on your monitor We recommend that you choose RGB when possible as there will be fewer surprises The colors will closely match what you s
326. on the clipboard Excel Windows 2003 and later and Excel Mac 2008 and later copy data to the clipboard in two formats Plain text and HTML By default Prism starting with 5 0c and 5 03 pastes the HTML format This will allow much better pasting of Greek letters superscripts and subscripts titles with punctuation numbers with nonstandard thousands or decimal separators and more There is one change If the Excel cell contains a mixture of numbers and letters or punctuation prior versions tried to extract and paste just the numbers Prism Mac still works that way but Prism Windows won t paste anything into numerical parts of a Prism table if the corresponding Excel cell mixes numbers and text This new style of pasting only applies when pasting values Paste embedding and paste linking Windows only are not changed Changing back to the old style 1995 2014 GraphPad Software Inc 168 GraphPad Prism User Guide 12 6 Pasting from the HTML rendition is the default If it causes any problems use Edit Paste Special and check the new option on the first tab x Paste older text based clipboard format Not recommended With this option selected pasting will work just as it did with earlier releases of Prism before 5 03 and 5 0c We don t anticipate any situations where this will be helpful but are providing this option just in case The option is available when you insert data only and will be unavailable if you
327. ontingency table analyses Survival analyses Parts of whole analyses i 2 Eeee 1995 2014 GraphPad Software Inc Analyzing data with Prism 319 Step 2 Analysis parameters dialog Each analysis dialog has its own parameters dialog Read about individual analyses to learn about the choices If you are unsure about an analysis choice click the Learn button in the dialog to go to the appropriate help topic Learn Step 3 View the results Prism places the results into new sheets in the Results section of your project These results sheets are saved with the project At any time in the future you can view the results review the analysis choices and change those choice to update the results Some results are presented on several sub pages Choose a sub page to view using the navigator on the left or the navigation toolbar at the bottom 7 Data with Raut a a a E p repl Equation Nonlin fit of X repl Table of results Equation Sal Curve fa Table of results Residuals L2 Curve Summary table L Residuals Interpolated Y values L Summary table Interpolated X mean values i Interpolated Y values Interpolated X replicates Laas i Interpolated X mean values L Interpolated X replicates Click the Analysis checklist button in the Interpret section of the Prism toolbar to review a list of questions that will help you interpret the results GraphP
328. onto the layout Choose 4 graph No Graph Assigned Pick a graph from another project Project4 Current project Fest look grouped dats Project3 Project2 Project Go To Jea ackground Linking Crop from Live link Update the layout when the graph changes Left 0 00 Unlinked picture Cannot be edited Right 000 n Merge a copy of the grap ath linked data mfo and results sheet Top 0 00 n Prefix for merged sheets Botton 0 00 in Help Cancel Choose a graph Note that you can not only choose a graph from the current project but a graph from any project It is especially easy to choose a graph from another open project If you choose to Pick a graph from another project that is not open after you choose that project file Prism will open it Linking within a project By default Prism the graph on the layout automatically updates when the graph itself updates You can choose to place the graph on the layout as an unlinked picture with no link to the original data You might prefer this option if you are sure the graph is 100 done and you don t want to allow any possibility of it being changed It can also be useful if you want to keep snapshots of a graph as a project continues and additional data are collected 1995 2014 GraphPad Software Inc Page layouts 363 and graphed Linking between projects If you choose or paste a graph from another project you ll have three choices
329. oose what you want error bars to show and how you want them formatted 11 1 Key concept Replicates and error bars When you collect scientific data you almost always collect replicate data and plot the individual replicates or an error bar showing the variability of the data One of Prism s strengths is its ability to handle replicates and error bars e You can enter replicates directly into a Prism data table If you enter replicate values Prism can plot either individual replicates or error bars You do not need to enter SD or SEM values in order to plot them Prism can plot error bars from raw data You do not need to run a Row Means analysis to plot error bars Prism can plot error bars directly from raw data See also Graphing each replicate Key concepts SD Key concepts SEM SD and SEM are not the same When to plot the SD vs SEM 11 2 Replicates and error bars on XY graphs Setting up data tables for entry of replicates or error values 1995 2014 GraphPad Software Inc 1 GraphPad Prism User Guide When you create an XY table choices on the Welcome or New Table dialog let you specify side by side subcolumns for entry of replicates or error values computed elsewhere Learn more about XY tables The example below is set for entry of two replicate values duplicates but you can choose any number from 2 to 256 Y O Enter and plot single Y value for each point Ene 2 replicate values in side by side
330. ordance with the laws of the State of California USA without giving effect to the conflict of laws principles thereof excluding the UN Convention on Contracts for the International Sale of Goods ENTIRE AGREEMENT This Agreement sets forth the entire understanding of you and 1995 2014 GraphPad Software Inc Support and license 467 GraphPad relating the subject matter hereof and supersedes any and all other previous or contemporaneous communications agreements representations warranties or advertising with respect to the Software and User Documentation SEVERABILITY The invalidity or unenforceability of any provision of this Agreement Shall not affect the validity or enforceability of any other provision of this Agreement If any provision of this Agreement shall be held invalid or unenforceable in part the remaining portion of such provision together with all other provisions of this Agreement shall remain valid and enforceable and continue in full force and effect to the fullest extent consistent with law NO WAIVER No term or provision hereof will be considered waived and no breach excused unless such waiver is in writing signed on behalf of the party against whom the waiver is asserted No waiver whether express or implied will constitute a consent to waiver of or excuse of any other different or subsequent breach LANGUAGE The English language version of this Agreement is legally binding in case of any inconsis
331. ormat be used by checking the option x Paste older text based clipboard format Not recommended Two ways to paste from the HTML It gets even more complicated With Excel 2003 the HTML clipboard version contains each number twice One copy shows exactly what you see in Excel The other copy shows the value with more decimal places ignoring formatting or rounding within Excel By default Prism pastes the values as they are shown in Excel But the Paste Special dialog lets you use the other version if you prefer x Paste as many digits as possible If Excel rounds to 1 23 paste 1 2 This option is not available if you copy from Excel 2007 or Excel 2010 as the necessary information is not copied to the clipboard It is also not available when importing from Excel Note a bug in Excel Mac 2008 In very rare cases using that option will result in the wrong values being pasted into Prism 1995 2014 GraphPad Software Inc GraphPad Prism User Guide How to interpret spaces and commas The choices are self explanatory but important 12 8 2 View tab The View tab of the Import and Paste Special dialog lets you see the contents of the imported or pasted file divided into columns This can be especially helpful if you are importing from a comma or tab delimited text file A quick look can let you know if your columns are formatted correctly P Import and Paste Special Choices Source View Fiter Place
332. orrect a mistake if you were actually entering SEM values but mistakenly set up the table with a subcolumn labeled for SD values Don t make changes in the Format Data Table dialog when you want to change the way the error bars are plotted Read on to see how to change error bar plotting Choosing how the replicates or error bars are plotted When you create a new table and enter replicates you choose not only how the subcolumns are formatted but also how Prism plots them You can choose to plot individual replicates mean only mean with error bar which you can specify Choose from a pair of drop down lists directly below the place where you choose the number of replicates If you choose to enter error values directly Prism will plot the values you entered except that when you enter CV Prism plots the SD If you entered Mean SD or SEM and N you can choose on the graph to plot the error bars as SD SEM or 95 Cl Changing how replicates or error bars are plotted To plot the replicates or error bars differently you don t have to remake a graph Instead click the Change graph type button Change L Li KON X ie amp The changes you make on the Change Type of Graph dialog apply to all data sets on the graph An alternative approach is to double click anywhere on the graph to bring up the Format Graph dialog Then click the All button so changes you make apply to all data sets If you don t do this you might accidentall
333. ot assume that the two sets of data before and after in the typical example are sampled from populations with equal variances W was the pairing effective The pairing should be part of the experimental design and not somethin 3 3 Everything is hot linked Prism links data to results and graphs This has three advantages e When you fix a mistake a data entry the results and graphs are automatically updated e When you open a Prism file you can retrace every step of every analysis and review or change any of the choices You ll never see a curve or a P value and wonder how it got there 1995 2014 GraphPad Software Inc a GraphPad Prism User Guide e h Data with Results hE Baseline corrected of Exeriment 34 F Transform of Baseline corrected of Exeriment 34 e After you ve polished the analysis and graphing steps with data from one experiment you don t have to repeat all those steps Prism provides several ways to instantly analyze and graph a repeat experiment without repeating any tedious steps and without requiring any scripting or programming Open a file LabArchives Clone a graph Graph portfolio 3 4 A complete record of your work Annotate your experiments with floating notes Add floating notes to data tables results and graphs x Minutes x Group A Control A Y1 A Y2 A Y3 8887 7366 a Record experimental details in Info tables 19
334. ote that there no value of L will result in a value of Z that is zero or negative Logarithms are simply not defined for zero or negative numbers Bottom line A logarithmic axis can only plot positive values There simply is no way to put negative values or zero on a logarithmic axis 1995 2014 GraphPad Software Inc Graphs Frame and axes 307 A trick to plot zero on a logarithmic axis in Prism If you really want to include zero on a logarithmic axis you ll need to be clever Don t enter 0 instead enter as a small number For example if the smallest value in your data is 0 01 enter the zero value as 0 001 Then use the Format Axis dialog to create a discontinuous axis and use the Additional ticks feature of Prism to label that spot on the axis as 0 0 15 3 4 Regression fits the data not the graph Choosing a log scale changes the way the graph looks but does not change the data values Linear or nonlinear regression fit an equation to your data Your choice of axis scaling does not affect any calculations The three graphs shown below represent the same data by linear regression The graph below has linear X and Y axes so the linear regression line appears straight l The graph below has a logarithmic X axis The curve you see is the results of linear regression It is the best fit to the equation Y intercept slope X The X values used by the linear regression are the X values you entered Graphing this linear regres
335. ou enter and it is up to you to keep track of how these values were actually calculated and to label your graphs accordingly Graphing each replicate The advantage of showing every replicate instead of error bars When making a XY graph Column graph or Grouped graph you don t have to plot error bars Instead you can graph each data point replicate This is often the best way to display variation as it shows your data exactly Don t plot mean or median with error bars too quickly Stop to think about whether a graph of the actual data would be more informative Specific Binding fmol mg Z3 4a 6 FH 100 420 146 Concentration nl XY graphs Choose Individual Replicates when you pick the error format for your graph 1995 2014 GraphPad Software Inc Error bars and replicates 157 Graph family XY Individual replicates Plot Each Replicate Aligned Z Column graphs Choose to make a scatter plot Change Graph Type Graph family Column v nii eet e Of Lei Grouped graphs Choose the Plot individual values tab Then choose any of the graph types 1995 2014 GraphPad Software Inc as GraphPad Prism User Guide Change Graph Type Graph family Grouped z ba Plot individual values Plot summary data Interleaved scatter Plot Mean z 12 Importing and exporting data 1995 2014 GraphPad Software Inc Importing
336. ou first create a layout page Prism asks you to choose an arrangement of placeholders But you are not stuck with this arrangement You can always go back to the Format Layout dialog by clicking its toolbar button or dropping 1995 2014 GraphPad Software Inc 364 GraphPad Prism User Guide Change and choosing Arrangement of graphs If you assign the wrong graph to the layout it is easy to replace Just double click on that graph in the layout and choose its replacement Or drag the name of the replacement graph from the Navigator and drop on to the graph you want to replace It is easy to add a new graph to the layout First resize and move graphs to make space for a new one Then do any of the following the first two choices are simplest e Drag a graph from the Navigator and drop onto a blank spot on the layout page Don t drop too close to an existing graph or you might end up replacing that graph rather than adding a new one e Go to the Graphs section of this project or any other and copy a graph to the clipboard Then go to the layout and paste e From the layout drop the Insert menu and choose Prism Graph Then choose the graph you want to add to the layout e From the layout bring up the Format Layout dialog by clicking its toolbar button or dropping Change and choosing Arrangement of graphs and choosing to add another graph to the layout 19 5 The size of graphs on layouts What is the scaling factor
337. ou switch from one sheet to another The backup files are also saved whenever you Save your work so the backup files can never be older than your project files When you quit Prism normally the timed backup files are deleted In case of computer disaster the backup files will remain on your hard drive When you restart Prism these files will automatically load so you can continue your work Note a potential problem After a crash the automatic backup system works fine if you launch Prism as an application But if you double click on the file you were working on then you open that saved file not the backup that Prism saved elsewhere If you need to find these files which have the extension PZB their location depends on which operating system you use Windows XP C Documents and Settings username Local Settings Temp Windows Vista or Windows C Users username AppData Local Temp 7 Mac OS Library Application Support GraphP ad Prism 6 Prism Backups Manual backups of Prism files Prism provides an unusual way to save backup copies of your projects Click on the Save Special button in the File section of the Prism toolbar and choose Save a Backup Prism will save a copy of your project to the location and name you specify perhaps to a network or CD drive Note the difference between Save As and Save a Backup When you use the Save a Backup command Prism doesn t rename the file you are working on it simply saves a copy of tha
338. ows versions have two digits after the decimal point i e 6 01 Mac versions have a single digit after the decimal followed by a letter i e 6 0b In most cases a problem is best demonstrated by attaching a particular project pzf file to your email We provide support for Prism not statistical consulting Your Prism license does not include free statistical consulting Since the boundary between technical support and statistical consulting is often unclear we often will try to answer simple questions about data analysis But don t push your luck While we are often willing to look over a completed analysis to offer our thoughts we won t analyze your data for you No phone support We ve discovered that we can provide much better support by offering it via email only We know that some companies use email only as a way to brush off customers and avoid providing support We are not like that We really do provide individual helpful answers to your email questions often within an hour or two GraphPad doesn t offer telephone support for several reasons e Our customers live all around the world but we re only here during business hours on the West coast e When we return your phone call you might be at lunch away from your desk or gone for the day If we leave a message it might start a round of telephone tag that could last for days e We often consult with contract programmers in a different country before answering
339. pe If you want to enter several lines press Enter between lines When you are finished click to select another tool or somewhere else on the page To enter a paragraph with automatic word wrapping Enter the first line or two using one of the text tool buttons and then click anywhere else on the page to create the text object Go back and click on your text You ll see knobs on the corners Drag the knobs to make the text object the correct width Don t worry about the height as it will grow automatically as you enter text Now double click inside the text object to bring back the insertion point and type your text Don t push Enter at the end of each line as Prism will automatically wrap the text as you type To add Greek letters international characters math symbols or Wingdings First be sure you have a text insertion point Then press the Greek button and choose a character from the menus provided a To add a constant from an Info table You can add a constant from an Info sheet in a text box Use the Insert Info Constant button on the Write section of the Prism toolbar Once you ve added an Info constant to your graph or layout double click to open the text box and add a label If you edit the Info constant the linked text box on your graph will be updated Writ va Tira Changing text To change font and size of text Standard toolbar buttons let you make text bold italicized underlined subscripted or superscript
340. pend an extension For et example ExportWMF F WMF 23 2 15 Exporting data results or info tables Commands ExportTable filename lt ALL gt Explanation If used from a data or results table this command exports the entire table The format will depend on the extension you give the file name Choose from tab delimited text txt comma delimited text csv or Prism XML xml If used from an info table and the filename is a txt file this command exports only the notes and not the info constants If the file name is an xml file then this command exports both info constants and notes If you want to export only info constants use the WSheet command instead 1995 2014 GraphPad Software Inc 432 GraphPad Prism User Guide If you choose the XML format and include the ALL option all data and info tables will be exported You can also export the values in a data table or results sheet to a table created by a Script 23 2 16 Writing to Prism text HTML XML or SQL tables Commands Table Prism datatable number lt CLEAR gt Table Text lt amp gt lt delimiter gt Table CSV lt delimiter gt Table HTML lt border gt lt width gt Table XML filename Table SQL datasource lt table gt lt login gt lt password gt lt CLEAR gt WTable column title row col lt subcol gt WTable column title text or F or YN NextRow EndTable OpenOutput filename lt CLEAR gt
341. per limit is greater than or equal to 0 5 P 0 1602 P 0 1367 P 0 0067 1995 2014 GraphPad Software Inc Simulating data and Monte Carlo simulations 341 Click OK and Prism will run the simulations Depending on the speed of your computer it will take a few or a few dozen seconds Step 5 Monte Carlo results The results of the simulations are shown on only one page since we unchecked all the options for reporting individual simulations in the Hits tab above Parameters Monte Carlo _ Simdan Parameters to tatadata Hes Numbers of simulations Simedation to repeat Simulate Column Data of Two way ANOVA not Number of simulations 1000 Append these bo esting results so the total number of srmdastions is 2 Random seed Arto Match another Monte Carlo simdstion postive integer The fraction of hits is 0954 For this example we defined hit to mean that the confidence interval included the true parameter value In other words the confidence interval for HillSlope included the true value used in the simulation in 95 4 of the 1000 simulated data sets Since these results depend on which random numbers Prism generates you ll get somewhat different results when you try to follow this example This is what you d expect for 95 confidence intervals and means that you can trust the confidence intervals in experiment of this design There is no need to consider fitting the logarithm of the Hill Slope instead fo
342. ph without changing font size This can be useful when the journal specifies both the exact graph size it wants and the point size of fonts Resize Graph s Resize the entire graph To 100 of its current size As large as possible Make the length of the X axis 3 00 in O Make the graph width 4 76 in Change point size of text proportionally Move to Center of page D Upper left corner of page Point of confusions Changing the size of a graph vs changing the zoom The Zoom buttons at the right end of the bottom toolbar let you zoom in or out as you work ona graph These controls only change the magnification you see on screen and do not change its size when printed or exported QQ Changing the length of the axes vs changing the size of the graph 1995 2014 GraphPad Software Inc 210 GraphPad Prism User Guide The first tab of the Format Axis dialog lets you choose exactly how long the X and Y axes will be The graph itself will be larger depending on what you choose for numbering and titles The graph object will also be larger if you place tables text drawings or images on the page Click the Resize Graph button in the Change section of the Prism toolbar to change the size of the entire graph object including everything placed on the graph page You can tell Prism to make the graph have a specified width Or you can tell Prism how long you want the X axis to be You can also
343. phPad Prism 55 A B c mo mnato meor 110 Global shared E En Es ES Ee eee j OM 8 4 l 8 J 8 176007 AEE eee Tele e agi sig 5 e 34176 007 1o 6 3 6 608 to 6 326 Ge 007 ta 2 476e 007 to 4716 00 Graphs Once you enter your data in a data table Prism automatically creates a graph You can customize any part of a graph Learn more R i Normalize of Transform of dose response Normalized data no mhyditor j 4 inhibitor 110 YTitle o 109 10 107 10 10 104 10 Agonist ORE At tte RAR cnt le lint tls My At Aon itt ch te tt tnt it Layouts Combine several graphs or other sheets in a layout for printing or publishing You also can send layouts directly to PowerPoint and Word Learn more 1995 2014 GraphPad Software Inc 56 GraphPad Prism User Guide Normalize of Transform of dose response Normalized data e wron wo nwo 110 T5 o o 10 104 10 W4 10 10 10 Agorest Transform of RIA example Transformed data Binding Percent of Conroy s88 2 o gi gge a A gaa Concentration M _ a N 4 5 Families of sheets What is a family Prism remembers the links between data tables info sheets analyses graphs and layouts Replace or edit the data and linked analyses and graphs will update We call the current sheet with all linked sheets a family of sheets See the sheets in the current family The navi
344. phs Format Graph dialog survival plots Use this dialog to change the look of all the points in a data set If you want to change the look of a single data point use the right click menu You can also change all the symbols in selected data sets Double click on any graph symbol or bar to open the Format Graph dialog 1995 2014 GraphPad Software Inc 260 GraphPad Prism User Guide em f Format Graph Appearance Data Sets on Graph Graph Settings Data set Survival of Three groupe Survival propottions Control lt gt Global Show symbols Color SER Shape Border color See 4 X Border thickness 2pt x Eror bars Color SEE Dir Both Style Thickness 1 pt Connecting line Cob Pattern v Thickness 2 pt X Show area fill Additional options Plot or Left Y ais J Show legend ever lege Right Y aas Label each point with its ro Change Graph Type Help Cancel Apply OK To change the settings for one data set Select a data set from the list and choose the symbols lines and error bars for that data set Then select another data set and choose settings for that data set Click OK to redraw the graph with all the changes Note that a fitted curve is treated as a separate data set To change all data sets on the graph for example to make all symbols larger Drop the list of data set names and choose Change ALL data sets Or click t
345. plication such as Word or PowerPoint Use different color notes for different things For example have one colleague review all yellow notes and another one review all the blue notes To add a floating note to a Prism sheet Sheet 2 e 26 New Click on the button on the Sheet toolbar Harvey Look at the number of 5 3 a o 3 2 2 w ta Ca Dog 25 e 20 GBB Homster ch te scatter te te Day 1 Day10 Day20 0 Day f To minimize a floating note iaj Click the Minimize button on a Floating Note to collapse the note Or just double click on the top border of the note To add a link to a web site E Drop the Note menu using the button in the upper left corner of a note and use the Create Link to add a hyperlink to a website or other document To change the color or delete a floating note Drop the Note menu using the button in the upper left corner of a note and select Note Color Make Audio notes for your colleagues who don t like to read Windows only If you have a microphone and speakers attached to your computer you can 1995 2014 GraphPad Software Inc GraphPad Prism User Guide record notes and attach them to Prism graphs and layouts You cannot add audio notes to data table results sheets or Info sheets To record an audio note Sheet 2 K2 x x JE New Click on the button in the Sheet toolbar This will open a recording session To play an audio note D
346. plotting area but rather the desired width of the entire graph object including any legends or drawings or objects Embed fonts EPS on Windows only When you export to EPS format using Prism Windows choose whether to convert the fonts to outlines Learn the pros and cons of the two approaches Prism Mac does not offer the choice of converting text to outlines Defaults Check an option at the bottom of the dialog to lock in your settings of format and options to use as the default for future exports To change the default exporting location use the File Locations tab of the Preferences dialog The differences between export formats PDF Prism s PDF files encode vectors and fonts not bitmaps so the resulting file can be stretched to any size with no loss of quality Export in PDF format when you can Unfortunately few Windows programs import pdf images and few journals accept them In contrast PDF is the preferred format for transferring images between mac programs Notes e If your graphs are in color you will need to choose between RBG and CMYK color model e You don t have to have Adobe Acrobat to export PDF files Prism creates PDF files on its own e When exporting several graphs or layouts you can choose to export all of them to one PDF file Or you can ask Prism to create a separate PDF file for each sheet TIFF This is a bit map format which means that your graph or layout is turned into a collection
347. ps 70 Graph type changing Graph adding to layout Graphics importing 376 Graphing use column titles Graphing use row titles Graphs cloning 94 371 392 392 422 194 192 224 244 218 143 143 275 195 363 131 133 471 GraphPad Prism User Guide Graphs exporting to fille 384 Graphs exporting to Word or PowerPoint 397 Grid lines equally spaced on axis 275 Grids for alignment 379 Grouped data tables 116 Grouping 379 Guides for alignment 379 H Hardward requirements 457 Hidden toolbars 75 Highlighting sheets 88 Hooking analysis constants 326 Horizontal vs vertical graphs 203 Import command 427 Importing Excel files 169 Importing options filter 175 Importing options info amp notes 179 Importing options placement 177 Importing options source 172 Importing options vew 174 Importing text files 169 ImportLink command 427 Individual replicates plotting 156 Info sheets 84 Inner fence 237 Insert and maintain link to data objects 172 Insert data only 172 174 Insert object 399 InsertData command 428 InsertDataLink command 428 Inserting pictures and objects 376 Instances Open multiple 76 sje JPEG exporting 384 JPG importing 376 K Key concept data tables 109 Key concept linking and embedding data 160 Keyboard shortcuts 142 ee Lab Archives 107 Lab notebook 107 LabArchives 107 Landscape vs portrait 203 Landscape vs portrait Graphs 409 La
348. pting 429 Syntax scripts 419 System requirements 457 Ti Tab key shortcut 142 Table CSV command 432 Table for a bar graph 124 Table for a scatter plot 127 Table HTML command 432 Table Prism command 432 Table SQL command 432 Table Text command 432 Table XML command 432 Tables printing 408 Tables Data tables in Prism 109 Tabs move between sections 71 Technical support 459 475 GraphPad Prism User Guide Telephone support why we don t offer 459 Template vs method 98 Templates 97 Templates savinginalab 451 Text 371 Text boxes 371 Text files importing 169 Text files working with 168 Text Using Word to add formatted text 374 Themes Colorschemes 199 Three segment axis 289 Ticks 283 TIF exporting 384 TIF importing 376 Tips 59 Titles of columns 131 Titles of rows 133 Titles on axes 298 Tooltips 71 Tooltips for navigation 70 Tours 10 Training 467 Transforming 348 Transparent background 394 Transposing data as you paste Mac 165 Transposing data as you paste Windows 163 Transposing data tables 355 Tree on left navigator 68 Tukey method for box and whisker plot 237 Two grouping variable tables 116 Two Prism windows 76 Two segment axis 289 TXT files importing 168 Type of graph changing 195 U Uncompressed 100 Ungrouping 379 Units transforming to change 348 Using different parameters 321 Using Prisminalab 448 V Versions of Prism 102 Vertical text proble
349. pty e Blue italics values are excluded ignored by analyses and graphs Use Edit Exclude values e A grouped data table can contain 256 data set columns and as many as 256 sub columns Error bars Prism will compute and graph error bars from replicate values placed in side by side subcolumns as shown duplicate values in the table above Specify the number of subcolumns when you create a new table You can also choose to create subcolumns formatted for entry of error values computed elsewhere Group A Group B Group C Group D Table foemat Grouped x Y T E Y alo ajojn 9 6 Contingency tables What is a contingency table Contingency tables are used to tabulate the actual number of subjects or observations that fall into the categories defined by the rows and columns of a table The rows and columns can be defined in different ways based on experimental design e Prospective You choose subjects based on exposure from which you define the rows Each column represents a different outcome e Retrospective case control Each column represents a different group of subjects identified based on presence or absence of disease Each row represents a different exposure they have had in the past Experiment Each row represents a different treatment group Each column represents a different outcome Cross sectional You select a group of subjects and then categorize them by exposure different rows and dis
350. r a line by linear regression the best fit line or curve is essentially a data set Prism automatically plots the line or curve on a graph but you can remove the curve from one graph or plot it on other graphs Treat the curves just as you would treat any other data sets e When you transform or normalize data the results appear on green data tables You can t edit these tables but the data sets on green data tables can be graphed like any other Data Sets on Graph tab of the Format Graph dialog The second tab of the Format Graph dialog lets you add remove and replace data sets on the graph and also change the front to back or left to right order of data sets 1995 2014 GraphPad Software Inc 1 GraphPad Prism User Guide rF Format Graph Appearance Data Sets on Graph Graph Settings The order of data sets in this list determines what happens when two data points overlap Dats sets placed higher on this kst wil be graphed in front of data sets lower on the list Dats sets plotted front to back ponse data experiment 1 Curve B inhibitce 1 10 Data on graph esponse data expenment 1 Curve Ano inhibitor Add i se response data experiment 1B inhditor 1 10 Replace Dose response data sxperiment 1A no inhibitor Remove Reorder Top Up Revere Ator Selected data set Nudge al ponts x 0 00 Y 000 dats units Graph faster Graph a tow skip rows graph another row i a
351. r loss of life h You may not attempt to to reduce the number of licenses that you need by use multiplexing or pooling hardware or software to pool connections reroute information or reduce the number of devices or users that directly access or use the software i You may not install the Software on network servers and may not use any kind of remote access software to control and view the software running on one computer from another computer or terminal ALL RIGHTS RESERVED Title to and ownership of the Software the User Documentation and all related intellectual property are retained by GraphPad and its licensors The Software is confidential and the Software and the User Documentation are copyrighted The Software and the User Documentation are licensed to you not sold All rights of every kind that are not expressly granted to you in this Agreement are entirely and exclusively reserved to GraphPad and its licensors LIMITED WARRANTY GraphPad warrants that as of the date on which the Software is delivered to you and for thirty 30 days thereafter the Software will provide the features and functions generally described in the User Documentation and that the media on which the Software is furnished if any will be free from defects in materials and workmanship under normal use Except for the foregoing the Software and the User Documentation are provided AS IS All warranty claims must be made during such thirty 30 day period
352. r means on scatter plots and the connecting lines on before and after plot Plot on which Y axis Specify which axis to use for each data set This is useful if you want to show different type of data on the same graph If you choose to plot on the right Y axis Prism will create that axis if it doesn t already exist Additional op Piet on Left Y axis Right Y axis Show legend Revert legend t umr Label sach point with its row title Legend Select Show legend to create a legend for this data set You can edit the labels in the legend Double click on the legend text and type whatever you like Use the Revert Legend to Column Titles checkbox in the Legend section of the Format Graph dialog to change the labels back to match the column titles This checkbox is only available if you have edited a legend s F Label each point with its row title On before and after plots and scatter plots you can choose to have X labels show on the graph to identify individual data points Check this box to include X titles on graph near each data point Select each label on the graph and drag it to move it where you want 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 229 14 2 2 Data set spacing on Column graphs Set the standard spacing between columns To change the standard spacing between individual bars and groups of bars go to the Graph Settings tab If you enter
353. r orientation In the All Ticks section in the Format Axes dialog To label axes with row titles instead of X values If you entered both X values and row titles on an XY data table you can choose to label the axes with Row Titles instead of Decimal numbers via the Format setting in the Regularly spaced ticks section of the Format Axis dialog If you do this Prism will ignore the X values entirely and use the row number top row is 1 as the X values when plotting values 15 2 3 Major and minor ticks Prism lets you show both major and minor ticks on an axis By default Prism auto matically sets the minimum and maximum range for an axis as well as the major tick interval Aeee ereere ane 0 50 100 150 To change the major or tick interval Double click on an axis to open the Format Axes dialog Uncheck the Auto box in the Range section and set the major tick interval in the Regularly Spaced Ticks section To show minor ticks Double click on an axis to open the Format Axes dialog Select an interval for minor ticks in the Regularly Spaced Ticks section Choose the interval for minor ticks between major ticks and whether you want regular or log spacing Select the number of intervals you want between major ticks not the number of ticks For example choosing four intervals creates three minor ticks To hide ticks Double click on an axis to open the Format Axes dialog In the All Ticks section choose None for Direction in t
354. r this experimental design Step 6 Try variations If the confidence interval for this result is too wide for your tastes it ranges from 93 9 to 96 6 go back and run this Monte Carlo simulation with many more iterations perhaps 10 000 The conclusion is specific to the experimental design and parameter values you chose Go back to the simulation and change the HillSlope to 4 0 Then change the Monte Carlo dialog to redefine a hit to mean that the confidence interval brackets the true value of 4 0 A hit is defined when the lower limit is less than or equal to 4 0 and the upper limit is greater than or equal to 4 0 With such a steep HillSlope the confidence intervals really are not accurate at all The 95 confidence intervals only include the true value 4 0 in 83 1 of the simulations Doubling the number of concentrations changing the increment of X values from 0 5 down to 0 25 in the X values tab of the Simulate XY data dialog solves this problem With so many data points the 95 confidence intervals contain the true value in 95 3 of the simulations 1995 2014 GraphPad Software Inc 32 GraphPad Prism User Guide 17 4 By varying the choices in the simulation dialog and seeing the effect via Monte Carlo simulations you can design better experiments Another example Here is another detailed example using simulations to find the power of at test Reference 1 Arthur Christopoulos Assessing the distribu
355. race an analysis chain when the result of one analysis is the input to another E Data mith Rests 5 Wi log dose vs response Transform of log dose vs response Ka Aormalize of Transform of log dose vs response 1E tonin fit of Normalize of Transform of log dose v a ee ir Equation Ie Table of results r vi 4 ae se nett hte ee ee Ae ee oe Leara a Ping pong flip back and forth between two sheets Click the ping pong button in the bottom toolbar to go to the previously viewed sheet Click again to return a amp 4 OL p E JG ka fi Data 1 oraph X Or 1995 2014 GraphPad Software Inc Getting started with GraphPad Prism st Highlight or annotate sheets you want to return to Click the highlight button and the sheet name will appear highlighted in the navigator and gallery Sheet Ox X 3eNew Annotate any sheet with a floating note then find all annotated sheets in a special folder at the bottom of the Navigator Sheet 2 Eo X hew Search for sheets If your project is large click the search button on the bottom toolbar to find all sheets that include specified text 4 gt eH P Graphing Tips Change the color or size of just one symbol or bar Right click on any symbol or bar and you can change its appearance apart from other symbols or bars in the same data set Or select a range of values in the data table and change the appearance of all sy
356. raphPad Prism User Guide automatically updated 5 8 Col Stats of Data 1 f Concentration a tS Mean 1 Mean 54 89 ft 9 Upper confidence imit 57 63 on Geometric Mean j Geometric Mean 54 58 g Lower confidence imit 51 83 gi Upper confidence imit 57 49 S a Quartiles gfF 25th percentile 5259 y Medan 56 05 75th percentile 58 68 2 10 00th percentile 44 95 gf 30 00th percentile 62 31 Gilg Range g Lowest value 44 41 g Highest value 64 00 Lagi Range 19 59 Eg QC Control lines kug Mean 38D 37 35 jog Mean 25D 43 20 ff Mean 15D 49 05 9 Mean 1SD 60 74 if Mean 25D 65 59 FF Mean 35D 72 44 a Ty Stats ig SD 5 847 SEM 1 308 gf N 20 00 JF Sum 1088 Unilink Example 2 Confidence interval of EC50 1995 2014 GraphPad Software Inc Analyzing data with Prism 333 4000 3500 3000 2500 2000 1500 1000 500 0 YTitle 10 10 107 106 105 104 10 XTitle This example shows grid lines at the EC50 along with its 95 confidence interval All three values were hooked from the nonlinear regression using Additional ticks and grid lines so will move if data are edited or replaced 1995 2014 GraphPad Software Inc 334 GraphPad Prism User Guide Choose a value from an info ot analysis constant This wil be a hot link to be automatically updated in the future A Nonlin fit of Normalize of Transform of Dose response dat 5 H no in
357. rated tab unless an alternative is specified in OpenOutput command If there is no row label as it is an optional parameter then a semicolon at the end of the command is ignored and has no impact WTBlock script command The WTBlock command has the same syntax as WBlock Note that the label is applied to each row as output which is each column in the Prism table WTBlock row s columns to include lt row label gt lt gt Examples Here are results of one way ANOVA followed by Dunnett s test from Prism 6 04 the results show two new columns that were not in prior releases Iway ANOVA Mulmple comparisons 1 Number of families 4 4 4 2 Number of comparisons per fam y 4 4 4 3 Alpha 005 T 4 4 5 Dunnes mukpie compansons test Mean Dit 25 Ci of diit Significant Summary Adusted P Vae JA 4 4 k 6 4 4 t 4 4 7 Control vs Treated 38 33 5238to 2429 Yes Treated nls iana ta at bo ana pA 8 Control vs Treated Antagonest 3 500 16 89 to 9 894 No ns Trested Antagonist 4 4 4 9 Control vs Treated Agorist 16 73 30 78 to 2 685 Yes je Trested Agorwst 10 Control vs Solvert Blank 1 733 1578 to 1231 No ns Solvent Blank 11 t m t 12 t 13 Test detats Mean 1 Mean 2 Mean Odt SE of ae ni n2 q OF 14 t 4 t 4 15 Control vs Treated 4467 183 00 38 33 15 339 6
358. reated by a single analysis of all the data The slope just appears steeper in the right half of the graph because the time scale is more compressed Example 2 Response Percent Dose e Left segment range 9 5 to 8 5 e Left segment length 12 of the total e Right segment range 8 5 to 2 5 e Right segment length 88 of the total To place 0 on the left segment create an additional tick label at X 9 and enter the text 0 Example 3 Temperature C y j k h C ll aaahansaneaaaasaaraaaaal j 16 24 4i s 64 72 Time in Hours e Left segment range O to 24 e Left segment length 50 of the total e Right segment range 48 to 72 e Right segment length 50 of the total 1995 2014 GraphPad Software Inc 22 GraphPad Prism User Guide The line was drawn by linear regression which automatically skips over the axis gap 15 2 7 Additional ticks and grids To create additional ticks or grid lines Double click on an axis to open the Format Axes dialog In the Additional Ticks and Grid Lines section set the coordinate on the axis where the tick or line should appear Check the box to show either a tick or a grid line If the coordinate is at a location where there already is a regular number or label the label you enter in the Additional ticks section is shown and the regular label will be hidden r Irar Aes e Frame and Origin Manis LetY axis Right Y ands Tiles amp Fonts
359. resize a graph when exporting Specify the width of the graph with all the other objects on the page in the export dialog Prism won t change the graph in Prism but will create the exported graph file to match your choices 14 Graphs Symbols bars lines and legends 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 211 Prism lets you customize every feature of a graph Change the shape color and size of graph symbols change the fill pattern and color of graph columns change the order that data sets are plotted 1995 2014 GraphPad Software Inc 212 GraphPad Prism User Guide 14 1 XY graphs Formatting symbols and lines Format graph XY Prism lets you customize every feature of a graph Change the shape color and size of graph symbols change the fill pattern and color of graph columns change the order that data sets are plotted Double click on any symbol or the background of the graph to bring up the Format Graph dialog See also Appearance of XY graphs Front to back order of data sets Use row titles to label data points Nudging XY data sets Additional XY settings Replicates and error bars on XY graphs 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 213 14 1 1 Appearance of XY graphs Format Graph dialog XY graphs Use this dialog to change the look of all the symbols in a data set If you want to change the look of a single data po
360. rmat Days Settings in the Format Graph dialog also let you make this graph Uncheck the option to Show Symbols and check the option to Show bars spikes 10 5 Choosing a table to create a scatter plot Prism offers six distinct types of data tables Three of these can be used to 1995 2014 GraphPad Software Inc 12 GraphPad Prism User Guide create scatter graphs XY scatter graphs With an XY data table each X value can have several replicates for every data set When you make your graph you can choose to show all the replicates on your graph instead of error bars Start with an XY table if you want to show all your replicates for each X value 400 300 200 0 10 20 30 Here is the data table for the graph above TEE Group A Group B P AY AV AY3 B Y1 B Y2 B Y3 1 31 4 36 39 25 EJ 49 EA 57 6 87 89 6 z 5 89 9 102 145 154 6 121 ISTE 254 269 231 8 187 14 9 289 296 271 1n To format an XY graph to show each data point as in the graph above click on the Format Graph button on the toolbar select Global to choose all data sets and choose to Show each Replicate To show mean and error instead choose Mean and Error from this drop down menu instead 1995 2014 GraphPad Software Inc Data ta bles 129 Format Graph Appearance Data Sets on Graph Graph Settings Data set Data 1 Data SetB zhi Style Appearance Each Replicate m Plt Stag
361. rmat Graph dialog Double click on the graph to open it e To change the color of just one data point right click on that point or bar and choose Format this data point e Change the color of axes in the first tab of the Format Axes dialog Double click on an axis to open it When you choose any color in Prism mac you use the standard OSX color picker O Page Background 0s BENS o Sky Clear Auto EE E e The toolbar at the top lets you choose one of five different approaches to choosing a color The example above shows choosing a crayon but the buttons above let you also use a color wheel color sliders to enter RGB or CMYK or choosing from a color palette 1995 2014 GraphPad Software Inc 202 GraphPad Prism User Guide 13 9 e The magnifying glass icon gives you a sixth way to choose colors by matching a color elsewhere on your screen Click on the icon then click on any color showing on your screen ok if it is a different application e The custom colors at the very bottom of the dialog offer a seventh way to choose a color Simply click on the desired color See below for adding colors to this palette e Once you choose a color in the color picker you ll also see it in the Prism dialog You don t need to click OK or close the Color Picker dialog e To add new colors to the custom color palette at the bottom of the dialog drag a color down from the large swatch on top of
362. roblem you ll get the same results as if you had entered raw data However this not the case if your data are unbalanced it is impossible to calculate precise results from unbalanced data entered as mean SD or SEM and N Instead Prism uses a simpler method called analysis of unweighted means This method is detailed in LD Fisher and G vanBelle details below If sample size is the same in all groups and in some other special cases this simpler method gives exactly the same results as obtained by analysis of the raw data In other cases however the results will only be approximately correct If your data are almost balanced just one or a few missing values the approximation is a good one When data are unbalanced you should enter individual replicates whenever possible Repeated measures two way ANOVA Prism cannot perform repeated measures two way ANOVA if any values are missing Prism beginning with Prism 5 works fine if there are different numbers of numbers of subjects in each group so long as you have complete data at each time point or dose for each subject Say you are comparing two groups control and treated measured at four time points It would be 1995 2014 GraphPad Software Inc 12 GraphPad Prism User Guide fine if there were more treated subjects than control subjects so long as each subject has data at all four time points But Prism can not analyze repeated measures two way ANOVA if one of
363. rrect for multiple comparisons e New multiple comparisons test Holm Sidak has more power than the Tukey or Dunnett methods but cannot provide confidence intervals e Dunnett s test can now can be computed with 256 groups Prism 5 was limited to 20 groups e For all multiple comparisons that create confidence intervals check an option and Prism will create a new graph with those multiple comparisons confidence intervals 1995 2014 GraphPad Software Inc a GraphPad Prism User Guide 95 Confidence Intervals Tukey Treated Antagonist Treated a Treated Antagonist Control ee Treated Control a 100 50 0 50 100 Difference between group means e Multiple comparisons after one way repeated measures ANOVA without assuming sphericity Prism 6 can compute confidence intervals from repeated measures one way ANOVA using two different methods The new method does not assume sphericity Instead of using the pooled variation from all the groups which depends on the sphericity assumption the multiple comparisons are computed using only the data in the two treatments being compared The calculations still account for the total number of comparisons but don t pool the variation in all groups e When performing multiple comparisons testing it can make sense to use a overall familywise significance threshold higher than 0 05 Prism 6 lets you set it to 0 1 e Main and simple effects for multiple comparisons after two wa
364. rs 75 Monitors using two 76 Monte Carlo analysis 342 Monte Carlo simulations 336 Monte Carlo simulations with scripts 415 Moving between sheets 68 Moving graphs 105 Moving objects 379 Multiple graphs exporting 384 Multiple graphs on layout 362 Multiple sheet selection 81 N Navigator 68 Navigator tooltips 71 Next 422 NextRow command 432 Nonspecific subtracting 351 Normalizing 353 Notebook LabArchives 107 Notes floating 87 Nudging XY graphs 221 Numbering of axis 280 Numbers rounding 145 1995 2014 GraphPad Software Inc Index 0 Object 399 Objects 379 Objects importing 376 Office 399 Offset axes 273 Offsetting or nudging data sets 221 OLE 399 404 One click export 397 One grouping variable tables 115 Open command 426 OpenOutput command Options 89 Options saving 100 Order of rows in data tables 135 Orientation of graphs 409 Orientation of tables when printed 408 Origin of graph 277 Orphaned results 322 Outliers 139 Outliers generating 336 outliers in box and whisker plots 237 P Page layout arrangement 360 Page layouts 362 Page layouts creating 359 Parameters dialog returning to 321 parts of whole graphs 266 Parts of whole tables 119 Paste command 428 Paste link 399 Paste special 399 Paste special options filter 175 Paste special options info amp notes 179 Paste special options placement 177 Paste special options source 172 Paste special options
365. rtable Network Graphics png mng Windows Bitmap bmp Graphics Interchange Format gif Scalable Vector Graphics Format svg PC PaintBrush pcx TruvisionTarga Format tga Microsoft Paint Format msp PhotoShop 3 0 Format psd Windows Icon and Cursor Formats ico Prism Mac can import TIFF tif tiff Windows Bitmap bmp JPEG jpg jp2 j2k jpx Macintosh Pict pct pict Portable Network Graphics png To place a border around a picture or object Click once to select the image or object in Prism Then drop the Change menu and choose Selected Object 20 5 Tips for moving objects around Selecting objects on the page When you work in the Graphs section of your project the graph itself as well as text legends drawings and imported images are all referred to as objects When you are working in the Layout section of your project each graph with all of its objects is grouped into a single object Images imported onto a page layout are also objects Images imported onto a graph are objects in the graph section but are part of the 1995 2014 GraphPad Software Inc GraphPad Prism User Guide graph object in the page layout section To select one object Point to the object and click the left mouse button To select a rectangle or oval click on its edge Prism displays knobs on the selected object To select several objects Hold down the Shift key while selecting
366. rting into another program The size you will see in the other program depends on how that program deals with the mismatch of dots per inch dpi between the file and on screen and also on what view zoom setting you have in that program It is easy to find out how large an image is in pixels and its dpi e Mac Double click to open in Preview and then drop the Tools menu and choose Show inspector e Windows Double click to open in Photo Viewer then drop the File menu and choose Properties This works for Windows 7 other versions are similar Clear transparent background What is a clear background Within Prism there is no distinction between having a clear background and a white background Both look identical on screen When you paste or export a Prism graph into another program a clear background will let colors and objects show through so Clear is not the same as White 1995 2014 GraphPad Software Inc Exporting images from Prism 395 The problem is that not all export formats support the concept of transparency and Prism doesn t support all formats The jpg and bmp formats simply have no concept of a clear background so those file formats simply don t allow for the possibility of clear backgrounds Note that Prism lets you set two separate colors for the background of a graph What Prism calls the background is the color of the page The plotting area color is the background color within the plotting
367. s Notes 1995 2014 GraphPad Software Inc 144 GraphPad Prism User Guide e You ll usually want to create a series in the X column of any XY table but you can insert a series in any column of any table e If you select an entire column before bringing up this dialog the dialog will default to creating a series with 500 000 values This can take a while Adjust the value a reasonable number Turn the X column into a series This option is a carryover from prior versions of Prism and we suggest you use the Insert Series command instead To turn the X column into a series 1 Create a new XY table 2 Enter at least one Y value or column titles so the table is not completely empty 3 Click the Table Format button at the upper left of the table or drop Change and choose Format Data Table 4 Choose to generate X values and enter the starting value and increment Format Data Table Table Format Column Titles Data table Kind of table xy J Show row biles Yi Aulomabe column wadhe x Enter X values Also enter X enor values to plot honzontal enor bars Generate X values as a serias tailing ae 0 00 in increments of 1 00 Y Enter and plot a single Y value for each point Enter 2 repkcote values in side byade subcolumns Enter and plot emor values calculated ebewhere Erter Mean SD N X Help Cancel OK 1995 2014 GraphPad Software Inc Data tables 145 Notes e On ol
368. s lines and legends 251 Control Treated Note the difference between Stacked and Superimposed below When the bars are superimposed each extends from the X axis to the value When bars are stacked each bar starts at the top of the one below mca mca 2500 Tag 4000 Taig 2000 mmi ppoe 2500 mmi pp 3000 4500 2500 2000 1000 4500 4000 500 ped 0 0 h y h y gt gt gt ef e ow NTERLEQVED STACKED mm cat 2500 ag 2000 aren 4500 4000 500 0 ty ty x gt gt gt ro a SUPERIMPOSED It sometimes is helpful to combine both stacked and interleaved bars on the same graph as below This is done by checking the option to stack the dogs data set on top of hippos and to make the cats data set grouped 1995 2014 GraphPad Software Inc 252 GraphPad Prism User Guide 14 3 3 Plotting order of Grouped graphs Data set order The two graphs in this example are identical except that the plotting order was reversed 700 aan ance 700 200 gt le Dect haat Red Black Yellow Red Black Yellow Click the Rotate Flip button in the Change section of the Prism toolbar to reverse the order of data sets on a graph Blt 1 K u i amp To fine tune the left to right order go to the Data Sets on Graph tab of the Format Graph dialog 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 253 Format Graph Appearance Data Sets on Graph Grap
369. s 2 and 3 were corrected in Nov 2013 to correctly explain what Prism does The Tukey whiskers always stop at the value of a data point and do not extenda all the way to the 75th percentile plus 1 5IQR or all the way down to the 25th percentile minus 1 5IQR With Tukey s method the whiskers always end at a value matching one of the values in the sample So the two whiskers are often not the same length The terms boxplot and box and whiskers plot are often used interchangeably although originally the boxplot was used to describe a plot with Tukey whiskers fences and the box and whisker plot was used to describe a plot where the whiskers extend down to the minimum value and up to the maximum value Five number summary The term five number summary is used to describe a list of five values the minimum the 25th percentile the median the 75th percentile and the maximum These are the same values plotted in a box and whiskers plot when the whiskers extend to the minimum and maximum The term outlier The term outlier has many definitions The individual points that are plotted beyond the whiskers of a box and whiskers plot are sometimes called outliers but this definition does not match the definition used by the Grubbs or other outlier tests How to create a box and whiskers graph by entering the minimum maximum median and 25th and 75th percentiles rather than entering the raw data Usually Prism creates a box and whiskers graph
370. s a file Then you can delete the data object and start over To select a single cell within a Data Object to copy to the clipboard It is difficult to select a single cell within a data object If you click ona cell in a data object you will select the entire object To select one cell within an object click on a cell near the object but outside of it Then use the arrow keys to move the selection inside the object to the desired cell If a linked file has moved If the linked text or Excel file is in a folder different than the Prism file Prism stores the absolute location of the linked file If the file no longer exists at that location Prism won t be able to find it so will not be able to update the data table However the imported values remain in the Prism file You won t lose any data if the link is broken If the linked text or Exel file is in the same folder as the Prism file It matters whether the Prism file is stored in the PZF or PZFX format If PZFX the link is absolute If the folder has a new name or has been moved to a new location the link is lost If the Prism file is in the PZF format then Prism will maintain the link to the Excel or text file that is in the same folder as the Prism file It doesn t matter if the folder has been renamed or has been moved to a new location 1995 2014 GraphPad Software Inc as GraphPad Prism User Guide 12 12 Exporting from data tables Copy and paste The best
371. s data into Prism When in doubt use Paste Link Paste Data Transposed Converts data in Excel rows into columns in Prism and vice versa e Paste Embed Transposed Converts data in Excel rows into columns in Prism and vice versa You can choose to paste data only and embeds a 1995 2014 GraphPad Software Inc Importing and exporting data 165 copy of the Excel sheet in Prism e Paste Link Transposed Converts data in Excel rows into columns in Prism and vice versa Retains a link to the original Excel sheet e Paste Special Opens dialog to let you choose whether to embed or link to the original file Windows only and also choose to filter and rearrange the data as you paste it into Prism The Paste Special dialog is identical to the Import dialog Pasting an Excel table as a picture You can copy a portion of an Excel spreadsheet and paste it onto a Prism graph or layout This pastes a picture only and Prism cannot analyze or graph the values since the values are not in any Prism data tables Optical Density Units 00 01 02 03 04 OF Protein mg mL Importing Excel files There are some limitations and we don t recommend it but you can import Excel files directly into Prism for Windows 12 4 Pasting data from Excel Mac Pasting data from Excel Select a range of Excel data and copy it to the clipboard Switch to Prism and move the insertion point to the cell of the data table that will bec
372. s is discontinuous a ake the Da ynimecting ine i ninu Format of individual points To format a data point differently than the rest eat this dialog nght click on the deta pont and choose Format This Pont ji the indrvidual formathng Revert all pants to the format of ther data set ChengeGreoh Type Hee Cancel C ae Set how you want the bars to be grouped You can change the overall grouping scheme of a graph or make hybrid graphs types using the order tab of the Format Graph dialog For each data set choose whether it should be interleaved with stacked on top of placed apart from the starting a new group of bars hence the name grouped or superimposed on the preceding data set 1995 2014 GraphPad Software Inc 250 GraphPad Prism User Guide Format Graph Appearance Data Sets on Graph T Graph Settings Order of bars from left to nght or bottom to top for stacked bars uped daa Contro tio el ted data set with the previous one Interleaved 5 Stacked D Superimposed Change Graph Type Help Cancel Apply Add lines between groups Check the box to Separate a data set from another with a line Space between selected data set and the previous one 100 of normal this data set from the price one with a vertical line Thickness 1p Styles wt wee Color Ato Under data points 7 1995 2014 GraphPad Software Inc Graphs Symbols bar
373. s it takes to reach a value So the log base 2 of 16 is 4 because if you start with 1 and double it four times 2 4 8 and 16 the result is 16 Immunologists often serially dilute antibodies by factors of 2 so often graph data on a log2 scale Cell biologists use base 2 logarithms to convert cell counts to number of doublings Logarithms using different bases are proportional to each other So converting from natural logs to common logs is sort of like changing units Divide a natural logarithm by 2 303 to compute the common log of the same value Multiply a common log by 2 303 to obtain the corresponding natural log Mathematical properties of logarithms Logarithms convert multiplication into addition and division into subtraction and exponentiation into multiplication log A B log A log B log A B log A log B log An n log A 1995 2014 GraphPad Software Inc 316 GraphPad Prism User Guide Antilogarithms The antilogarithm also called an antilog is the inverse of the logarithm transform Since the logarithm base 10 of 1000 equals 3 the antilogarithm of 3 is 1000 To compute the antilogarithm of a base 10 logarithm take ten to that power To compute the antilogarithm of a natural logarithm take e to that power The natural logarithm of 1000 is 6 980 So the antilogarithm of 6 908 is e608 which is 1000 Spreadsheets and computer languages use the notation exp 6 908 Terms that sound sim
374. s of a large number of files or simulate many data sets for Monte Carlo analyses Prism s scripting language lets you open and close Prism files import data and export or print results and graphs You can run Prism scripts from within Prism or launch Prism from another program Note that Prism scripts do not tell Prism how to analyze or graph your data That is built in to the Prism project or template Use a script to import data into an existing project and to specify which results and graphs you want to export or print Scripts are small computer programs Creating a script is slightly more difficult than using Prism Experience with other scripting or macro languages is helpful but is certainly not necessary If you want to launch a Prism script from Excel you will also need to learn a bit about Excel s macro language Visual Basic for 1995 2014 GraphPad Software Inc aa GraphPad Prism User Guide Applications To learn about scripts first look over the examples we present in the next section These examples show you the kinds of things that Prism scripts can do and give you a feel for how easy it is Then read on to learn the details of Prism syntax The final sections of this chapter explain how you can launch a Prism script from another program 23 1 2 Script example 1 Repeatedly import data This script analyzes a folder full of dose response data stored as text files perhaps from an instrument It creates a sing
375. s that the data are censored after the specified X time value Negative values are impossible Situations where fractional values can become integers when imported or pasted into a Prism table e In a contingency table the rows denote treatment or exposure and the columns denote alternative outcomes Each value is the actual number of subjects objects or events Thus all values must be positive integers or zero If the data you are importing or pasting has a decimal point this will be ignored so 1 23 will paste or import as 123 If you want to include numbers of fractions you are not really creating a contingency table Drop the Change menu choose Format Data Table and choose a different kind of table You probably want a Grouped table e The Y columns of survival tables hold simple code values Usually 1 means death or some other event happened and 0 means the data were censored You can change the code but Prism can only accept integers into the Y columns of survival tables e Number format can depend on where you or whoever made the text file lives Acomma sometimes denotes thousands but sometimes is a decimal separator If you have trouble use Edit Paste Special instead of plain Paste The first tab of Paste Special dialog which is identical to the Import dialog lets you define what commas mean Commas To separate adjacent columns 100 000 mean one hundred in one column zero in the next To delineate thou
376. s the entire Prism project This might be useful if you send a document to a colleague and want to include all supporting details How to choose to paste an object a link or a picture One click buttons to send to PowerPoint or Word Choices in Prism s preference dialog determine whether Prism s one click Send buttons send an object a link or a picture g Preferences gt ae Views File amp Printer New Graphs Analysis Internet Into Sheet Send to MS Office Pend a graph or layout to Ward or PowerPoint as Embedded object recommended Linked object Only for MS Office XP or greater Picture only No link mage EMF vs WMF format on the FletPrinter tab Wapping style in Word Use Word s default Ful page width rmine Lett side of page floating wrap text on the right Aight sde of page floating wrap text on the left Graph or layout colors in Word Ful colos same as in Prism Monochrome black and white no gray Grayscale Border within woed Draw a box around the graph No box Note These options apply when you use the Send to Word or W Send toPowerPoint command or buttons but do not apply when pou copy and paste Copy and paste 1995 2014 GraphPad Software Inc s GraphPad Prism User Guide When you copy a graph or layout Prism put all the necessary information on the clipboard so the pasting program can choose ff it wants to paste a picture
377. s will need to be recomputed when the file is opened which can take time Zipping the file with standard zipping software can do a much better job of compression To really make a file as small as possible save it compact and then zip it Check the box in the Preferences menu if you want to save in compact format as a default File Format PZF PZFx Cannot be opened by Prism 4 but data and info are in XML format that other programs can access L Do not save or read page size to or from pzf file a Save compact smaller but requires recalculations afte opening J Always prompt when saving to a temporary folder Saving vs exporting Saving and exporting are different When you Save your Prism file you save it in Prism s file format This type of file can only be opened with Prism Use Export to save a graph or layout in an image format that can be imported to another application If you export a graph or layout you are simply creating a picture of it You won t export the original data or any analysis results You won t be able to open the exported file or edit it except as a picture If you export a data table as a text file you are just exporting the values Saving as a template example or method To automate your work save a Prism file as a template as an example you will later clone or as a method that you can later apply to a new set of data 8 2 File compatibility between Prism versions
378. s you how many standard deviations you need to go above or below the mean for a cumulative Gaussian distribution to contain that fraction of the entire population Multiple by the standard deviation and add a mean and you ll have random numbers drawn from a Gaussian distribution with that mean and SD For example use this formula to sample from a Gaussian distribution with a mean of 100 and a SD of 15 NORMSINV RAND 15 100 18 Transforming normalizing etc 1995 2014 GraphPad Software Inc 346 GraphPad Prism User Guide Before graphing or analyzing your data you may first need to do some calculations to get your data into proper form While Prism is not as versatile as Excel Prism can do many data manipulations 1995 2014 GraphPad Software Inc Transforming normalizing etc 347 18 1 Key concept Manipulating data Before graphing or analyzing your data you may first need to do some calculations to get your data into proper form While Prism is not as versatile as Excel Prism can do many data manipulations From the data table click Analyze on the toolbar and choose transform normalize transpose prune or remove baseline p Data arp 4 k Built in analysis X Which analysis Analyze which data sets Transform Normalize a J A no inhibitor 7 B inhibito 1 10 Normalize Prune rows Remove baseline and column math Transpose X and Y 3 XY analyses Noriinear regress
379. same goal by going to a layout dropping the New button and choosing to Duplicate Family This will duplicate not only the layout but all graphs on the layout and all 1995 2014 GraphPad Software Inc seo GraphPad Prism User Guide results and data sheets linked to those graphs Edit all the data tables and you are done The analyses and graphs will automatically update 19 2 Choosing the initial arrangement When you create a new layout you can choose any number and arrangement of graphs create New Layout Add one more graph to the page Blank layout foe drawing and image layout Anay of gaps 12 across by 2x down Standard arrangement a Asrangemert of graphs 1 US e MEME Page options Onentation Potrat Landscape Background colce X Include master title on top of page Heb Cancel OK Here is a sample layout with four graph placeholders 1995 2014 GraphPad Software Inc Page layouts 361 To return to the dialog to choose a different arrangement of placeholders graphs click the Layout button on the Change toolbar Change 1995 2014 GraphPad Software Inc s2 GraphPad Prism User Guide 19 3 Assigning a graph to a placeholder Place Graph on Layout es Assign Graph Size and Location You don t need to use this dialog to place a graph from the currert project orto a layout Instead just drag the graph from the navigator and drop
380. sands 100 000 means one hundred thousand O As decimal place 100 000 means one hundred point zero zero zero 12 10 Unlinking data objects When a block of data on a Prism data table is linked to another file or to embedded data the data in Prism is included in a box The box is black if the 1995 2014 GraphPad Software Inc Importing and exporting data as linked data came from outside of Prism red or green if the data were paste linked from a Prism results table and blue if the data were paste linked from a Prism data table You cannot edit these values in the data table because they are linked to another source To unlink the data block and allow editing right click anywhere within the block of data choose the Data Object command and then choose Unlink 12 11 Changing linked and embedded data Blocks of Prism data linked to a text file or linked to an embedded spreadsheet Windows only appear with a border around them These are called data objects You cannot edit these values within Prism When you click on any cell within a block you select the entire data object The figure below shows a data object Table format X Group A i Minutes Treated To edit the data Double click anywhere on a block of linked data to bring up the Import and Paste Special dialog Then click Open File to Edit Data This will open your original Excel file After editing and saving the spreadsheet return to Prism an
381. scsttesorcscateesecessceussscsteiesseosersscvecasessecerssucesecehtensacscasentecevsuersiecttedeveses 429 Exporting a graph Or layout cccseceeseeeeseeeeseeeesaeeeeneeeseeeeaeeseaneesaeeensaeeseaeeesaeeensaeesaeeesaeeeneaeessaeeeseeeensneeesaees 430 Exporting data results or info table 0 0 0 eeescseceseeseeeseeeeeeeeeeeneeeseeeneaeeeeaeeesaeeeesaeessaeeeeaeeensaeessaeeeseeessaeensaees 431 Writing to Prism text HTML XML or SQL tables wee 432 Writing t t xt files i accicessceccscessccesseeceeecesscisedteseseecedsecoccsevencsccttcienssssenntuessevenctevsuceussacucssceresercedsccecevessnctssbietentivass 433 The WBlock and WTBIOCK com MAMAS 1 cceecceeeeeeeseeeeeeeseneeeeeseeseaeeeeseeeeeesaeneesesaensseesseessaeesesseseeeseeessenenetoneas 435 Send to Micros oft Office sssaaa eaaa an Aaa geaveuid manuetendnvaneneensteveneivedreereien 438 Special PUrPOSe command S wiccsicicscccacciccessrsscsesscecessessesseressctssrcsesecessuasestetsesserssccnseasessensesvcseteressnevesscrsceeeesens 438 Running lt a Prism SCript sssini raaraa ai aaa aaea eo i ena iaaa aa a a aani aaea aeai 439 Creating and running a script from Prism 440 Run a script using Automator MacScript or AppleScript ccessccsseeeeseeeeeeeeeeeeeeeseeeeseneeseeeeneeeeneaees 441 Launching a Prism script from outside Prism Windows cs ccesseeeseeeeeeeeeeeeeeeeeeeeeneeeeaeeeseeeeneeeeeeaees 443 Using Prism serpi WIth EXCe ligscsscccsccecesccsesessen
382. se the row number is ignored Examples SetInfo 5 3 3 Setinfo Notebook 25 page 34 5 Setinfo Experimenter 3 0 1995 2014 GraphPad Software Inc 430 GraphPad Prism User Guide Setinfo Dennis 3 1 Setinfo Notebook 2007H page 304 1 2 The first example sets the third constant equal to 5 3 The second example sets the fifth constant to Notebook 25 page 34 The third example names or renames the third constant to experimenter The fourth example assigns the value Dennis to that constant The fifth example adds some text to the notes portion of the info page With the SetValueToInfo command the value comes from a data results or info table Navigate to that table first Then specify the row and column of the cell with the value you want and which row of which info table you want to paste that value into 23 2 14 Exporting a graph or layout Commands ExportWMF filename lt CLEAR gt Windows only ExportEMF filename lt CLEAR gt Windows only ExportPICT filename Mac only ExportTIF filename lt resolution gt lt mode gt lt compress or LZW gt lt clear gt ExportBMP filename lt resolution gt ExportPNG filename lt CLEAR gt ExportJPG filename lt resolution gt ExportEPS filename lt mode gt lt clear gt lt nofonts gt ExportPCxX filename Windows only ancient format avoid using it ExportPDF filename lt mode gt lt clear gt Explanation For the
383. se data expenmert 1 Curve 4 no inhibitor dd se response data experiment 1 B inhibitor 1 10 E Dose response data experiment 1A no inhibitor Replace Remove Selected data set Nudge al ponts x 0 00 Y 200 data units Graph faster Graph a row skip rows graph another row Change Graph Type Cance App See also Nudging data sets on a graph 1995 2014 GraphPad Software Inc 220 GraphPad Prism User Guide 14 1 3 Use row titles to label data points Infant Mortality vs GDP e Sierra Leone IMR oBSSSEREBS et a3 eee Venezuela United States of America e 9 E ee Span Japan te ptg geet o 0 5 000 10 000 15 000 20 000 Real GDP per capita Enter row titles in a special column on the XY data table Change fii EKDA K ty amp Click on the Format graph button on the Prism toolbar or double click on any data point to open the Format Graph dialog Check the Label each point with its row title box to include row titles on graph near each data point Additional options Plotorc Left Y ais Show legend Spmbol amp Line X You can move each label by selecting it and dragging Even if you move a label however Prism remembers its position relative to the data point so when you change your data or the size and shape of your graph the labels will adjust accordingly Click on any label on the graph and use the Text
384. seceseuessesaceuseisasesesensusionsdcearedsoaceasecerscvesbacssaseidsgueasetaresestsaverveaters 445 How long Can a Seript De isi ccsccccssceiseessissusclesvexeeivesvscccuecvectesucteescovsnsencuccceecetessthsvsevedetetexsstessvedetersuetesvacretscets 447 Standardizing Prism use in a lab 448 Locking the preference fil ccciiccceceiecovcecis cseeeiincetecsiecevesiincdueisen ca vevive coversdeessevein cou civencaveeeie 449 Individual preference fil Sinia aa send E a dansauseadevcg iaaa Ea ae 451 Shared templates methods and ExXaMples cccccscccecesseeseeeeeeeseeeeeceeeseeeseeeseeeseeeseeeages 451 Adding your own built in CQUaTIONS ccceecee cece eee eee eeeee ee eeee nessa eeeeeeeeaeeeeeeeeeneneeneneeeeanes 454 Using a local LabArchives Servel cccceeeeseeceeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeneeseeeeeeeeeeeeeeneneeennnes 455 1995 2014 GraphPad Software Inc Contents 9 Part XXV Support and license 455 1 System Require me tsi a2 ic cso cceceetce tcc cscteees cesticectdeceetcnvesadecauesvescentyasecduaschieenovacccduesves nnmnnn 457 2 Command line switches Windows OMLy ccceeeceeeeeeeee seen ee eeeeeeeeeeeeaeeeeeseaeeeeeesaeeeeeesaneeeees 457 3 Technical SUPPOM eis citsecde si acces aa a a a A aa vive davudevec EA E E EAEn 459 As How toCite Prismarine a iaa aara Aaaa aanas aaar aaae aana ra adea raaa irana 461 5 GraphPad Prism license agree Ment cccecececeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeee
385. section e Prism numbers the sheets so the first sheet is 1 This seems normal to everyone except computer programmers who expect the first one to be 0 e Don t forget to include a space or comma between the results and the view The command GoTo R4V2 goes to the default current view of results sheet 4 and the view part of the command is ignored 1995 2014 GraphPad Software Inc 23 2 2 How rows and columns are numbered Many commands let you specify a particular row or column number Column numbering e The Row Title column if there is one is number 1 e The X Column if there is one is number 0 e Column A is column 1 e Column B is column 2 etc Row numbering e The Column Title row if there is one can be referred to either as row O or 1 to be consistent with column titles e The other rows follow the row number shown on the table So the first data row is 1 This seems obvious to most but people familiar with other computer languages may expect the first row to be 0 23 2 3 Adding comments to a script Add comments to your script following these examples Commands single comment line Several lines of comments 1995 2014 GraphPad Software Inc 42 GraphPad Prism User Guide 23 2 4 Loops and simulations Commands ForEach of loops ForEach filespec i e C data DR txt ForEachSheet Next Regenerate Explanation The heart of many scripts is a loop You can
386. section of the Prism toolbar to change the size font and color of all the labels You cannot adjust the font individually All the row labels always share the same font size and color 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 221 14 1 4 Nudging XY data sets Nudge overlapping data sets to make a graph easier to understand Double click on any data point to open the Format Graph dialog Use the bottom of the Data sets on Graph tab to nudge a data set Nudging adds a specified value to each X and Y coordinate before graphing Use this feature cautiously as it means that the position of the symbol on the graph will not match the actual X and Y values of the data point Selected data set V Nudge all points x 0 00 Y 50 00 data units The values you enter are the actual increments of X and Y Each data set is incremented as much as you specify The nudging is not cumulative Nudging can be helpful to differentiate datasets that otherwise overlap a lot For example the data in the following graph overlap so much it is impossible to tell which tracing is which millivolts Seconds The graph below is an alternative way to plot the same data The second data set is nudged by 25 units in the Y direction and not at all in the X direction Selected data set Z Nudge all points gt 0 00 Y 25 00 data units The third data set is nudged 50 units in the Y direction with zero in the
387. sing mported fie nan Text Column titles Choose automatically ed Top left position of inserted data within Pram The curent position of the insertion point Row Column Row and column atrangement Maintain tow and column arrangement of the data source Transpose Each row becomes a column By rows Place values on each row fte rows stait a new column By cokwnns Stack values in each column Empty rows If all values in a row are blank leave a blank row in Prism skip over that row Use these settings as the defauk for Import and Paste Special Restore ongnal default Help Cancel Paste Names The Placement tab lets you choose whether you want to rename the Prism data table and or the Prism column titles with the name of the imported file or with text imported from a specified row in that file Top left position of inserted data within Prism Specify the top left corner of the data object in Prism Normally this will be the position of the insertion point when you choose the Import or Paste Special command but you can change it Row and column arrangement Prism can rearrange the data as it imports If you choose Transpose the first row in the source will become the first column in Prism the second row in the source becomes the second column in Prism and so on If the data source has one column or row and you want to organize the data according to your experimental design choose By rows or By columns
388. sion line on a log axis results in a curve SERSEOEE 1995 2014 GraphPad Software Inc 308 GraphPad Prism User Guide Pi The graph below has a logarithmic Y axis Again the best fit linear regression line appears curved when plotted on a logarithmic axis RRRARARE 100000 10 100 5 00 o oo a00 eo 300 400 500 15 3 5 When to use a logarithmic axis A logarithmic X axis is useful when the X values are logarithmically spaced The X axis usually plots the independent variable the variable you control If you chose X values that are constant ratios rather than constant differences the graph will be easier to view on a logarithmic axis The two graphs below show the same data X is dose and Y is response The doses were chosen so each dose is twice the previous dose When plotted with a linear axis left many of the values are superimposed and it is hard to see what s going on With a logarithmic axis right the values are equally spaced horizontally making the graph easier to understand 1995 2014 GraphPad Software Inc Graphs Frame and axes 309 g 1000 id fd o o F F g LS 500 x 0 0 2000 4000 6000 8000 10000 0 1 1 10 100 1000 10000 Dose in nM Dose in nM A logarithmic axis is useful for plotting ratios Ratios are intrinsically asymmetrical A ratio of 1 0 means no change All decreases are expressed as ratios between 0 0 and 1 0 while all increases are expressed as ratios greater
389. sm and run a Prism Script e Choice of color model RGB CMYK or Grayscale when exporting JPEG e Choice to compress when exporting tiff at high resolution e Export in PICT format File compatibility Files saved on one platform can be opened on the other In almost all respects this just works and you don t have to think about it But there are three exceptions e If you use Prism Mac and copy a graph from one project and paste it onto a layout on another project Prism can handle this in two ways By default it pastes in a form that works only with Prism Mac If you open the project in Windows that graph will be missing from the layout Use an option in the Files tab of Prism Preferences to save in a compatible format On the Mac you will notice that the files will be larger and pasting graphs from other projects noticeably slower but still only a few seconds Now the file will open fine in Windows e If you dictate audio notes to embed onto a graph or layout of Prism Windows those audio notes will not be present when you open the file on the Mac e Tabs within titles or text objects are handled differently on Windows and Mac If you include tabs within text objects the spacing of that text may change a lot when you open it on the other platform 5 Getting around in Prism Prism is easy to use Use the Navigator tree to 1995 2014 GraphPad Software Inc Getting around in Prism move between parts of a projec
390. smaller but requires recalculations after opening F Always prompt when saving to a temporary folder Print Options Print grid lines on tables E Print no grays and no colors T Print row and column labels T Print sheet name as header Copy to clipboard Copy graphs and layouts as Both WMF and EMF om Background color Include when copying Copy excluded values Numbers followed by Decimal separator Period z Sending to PowerPoint Rather than copy and paste we urge you to use the Send to Powerpoint command a button at the right end of the toolbar or a command in the File menu The choice you make for sending background color to the clipboard see prior section also applies when sending a graph or layout to Powerpoint When you copy a graph or layout from Prism Mac two versions are placed onto the clipboard The PDF version supports transparent background and plotting area Whether the background is clear or not depends on an option you set in Prism s Preference dialog bottom of File amp Printer tab The bitmap version does not support a clear background If you copy and paste which version pastes depends on your version of PowerPoint and on whether you use Paste Special 1995 2014 GraphPad Software Inc Exporting images from Prism 397 Avoid the uncertainty by using the Send to Powerpoint command 21 9 One click to Microsoft PowerPoint or Word Send to PowerPoint or Ke
391. so find this command if you drop the Save menu from the toolbar 4 On the Save Template dialog choose or create a category folder enter a name for the new template and optionally enter a description and or instructions for using the template If it will be used by others you can write a help file for it and install the files onto other computers To use a template You ll see a list of templates on the Open a File tab of the Welcome dialog When you open a template any description of instructions you entered will appear in a popup dialog Templates on your own The instructions above assume that you save the template from Prism and open it via a link on the Welcome dialog But you can rename any Prism file to have a pzt extension and open it from Windows Explorer or Mac Finder by double clicking on it The difference is that when Prism opens a pzt file it instantly forgets the file name so will prompt you for a file name when you first save it 7 5 Template or method wand When you want to analyze and graphs a set of experiments the same way you can save your example as either a template or method In either case start from the data table drop the File menu choose Save Special and then choose Save Template or Save Method 1995 2014 GraphPad Software Inc Work efficiently Repeat analyses and graphing 9 The difference is in when you choose to use these files e Open the template from the Welcome dialo
392. ss Check the Clear option if you want point to point lines and overlapping points to show through the open symbol Click More to use any character from any font as a symbol 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 247 Shape See 00a 090090 ines SOR ODGOR AVAVAAVY POSS OHO 050 0308 X O 9g C Mae gt ee eee ee ee eee wve oanp If you choose to plot your data sets as bars columns box and whiskers or floating min max boxes choose the color outline and fill of the bars and boxes Use the Data Sets on Graph tab to adjust the spacing between bars and whether you want the bars stacked interleave grouped or superimposed Prism labels bars with the row titles from the data table You may not edit the bar titles directly but if you edit the row titles the graph will update Use the Format Axes dialog not the Format Graph dialog to turn off the labels or to change to vertical or angled labels If your data table has only one row Prism will place the column titles rather than row titles under each bar Format error bars Choose the format and color of error bars Learn more about error bars on Grouped graphs Lines Choose the format of lines connecting data points for a before and after plot Consider using arrows Plot on which Y axis Specify which axis to use for each data set If you choose to plot on the right Y axis Prism will crea
393. started with GraphPad Prism e Click one button and you are done No need to copy and paste or export and import Send gaz Experiment with copying graphs in EMF or WMF format Windows only By default Prism copies graphs to the clipboard in both Windows Metafile and EMF Enhanced metafile format and lets the pasting program decide which one to use You can tell Prism to only copy one format File amp Printer tab of the preferences dialog If graphs pasted into other programs don t look right try all these settings Copy to clipboard Copy graphs and layouts as Both WMF and EMF Background color WMF an Choose export formats carefully Prism offers a variety of formats When possible choose formats that include information about vectors and fonts WMF EMF PICT EPS PDF over formats that only describe bitmaps TIF JPG PNG Send your colleagues complete Prism files rather than exported images Anyone can view the complete Prism file including analysis choices using the free Prism Viewer which never expires Organizing tips a Rename reorder and delete sheets You aren t stuck with the sheet names that Prism assigns or their order Rename or reorder your data tables and graphs When you rename data tables linked analyses and graphs are automatically renamed Delete sheets you no longer need Highlight sheets you want to return to You ll see the yellow highlighting in both the navigator and gall
394. stead click the Change graph type button Change GLE LS a i gt d The changes you make on the Change Type of Graph dialog apply to all data sets on the graph An alternative approach is to double click anywhere on the graph to bring up the Format Graph dialog Then click the All button so changes you make apply to all data sets If you don t do this you are able to plot some data sets one way and other data sets another way 1995 2014 GraphPad Software Inc 154 GraphPad Prism User Guide If you plot the 95 confidence interval as confidence bands you can fill or color the area between the bands 11 7 Confidence and prediction bands from regression When you fit a line with linear regression or a curve with nonlinear regression you can choose to plot confidence or prediction bands Confidence bands tell you how precisely you have determined the line or curve Prediction bands tell you about the scatter of the data Learn more about choosing and graphing prediction and confidence bands from linear regression and nonlinear regression Prediction and scatter bands are computed using complicated calculations that are part of the regression procedures You don t enter these values directly All you do is check an option when choosing analysis options 11 8 Graphing error bars calclated elsewhere Choosing to enter precalculated error values When creating or reformatting a Grouped or XY table you can choose
395. subcolumns sanin Eoen paiese res z Mean only N te calc lsewhere Enter and tear end Ena p calculated elsewhere Erk p Median only z Median and Error I h a This next example is set up to enter mean SD and N for each point Y Enter and plot a single Y value for each point Enter 2 replicate values n side by side subcolumne and plo Each Replicate digned Enter and plot error values aleady calculated elsewhere Enter ee Mean SD N Availabi Mean SEM N Mean CV N Linear reg e Mean amp SD Nonlinear rE Mean amp SEM Correlation Mean amp XCV Organizatia Mean Error Mean Upper Lowes Limit WESS CV is the coefficient of variation which is equals 100SD Mean If you enter the CV Prism will plot SD error bars If you enter N along with the SD SEM or CV choose to plot the SD SEM or 95 CI via choices on the Format Graph dialog If you omit N Prism can only plot the error value you entered Changing the subcolumn format Click the Table Format button in the upper left corner of the table to reformat a data table change the number of replicates or change the entry of error values 1995 2014 GraphPad Software Inc Error bars and replicates 149 x Group A Use the Format Data Table dialog to specify how you will enter the replicates or error values If you change from entry of mean and SD to entry of mean and SEM only the labels change not the numbers This lets you c
396. sured values or percentages or normalized 19 Page layouts 1995 2014 GraphPad Software Inc 358 GraphPad Prism User Guide Page layouts let you combine several graphs on a single page along with data or results tables text drawings and imported images Graphs can be from one or several Prism projects 1995 2014 GraphPad Software Inc Page layouts 359 19 1 Creating layouts Create a new layout Click the New button on the toolbar or drop the Insert menu Sheet 2 AR Choose New Layout and select the format how many placeholders you want on the page and whether you want portrait or landscape orientation for the overall page Don t worry too much about your choice you can always change it later r Create New Layout dd one more g the page Blank layout foe drawing and image layout Anay of graphs 2 actossby 2 down Standard arangement Asrangemert of graphs Emit Baek Page ophons Onentation Potrat Landscape Background color X Include master title on top of page Heb Cancel Duplicate a layout If you have a page layout whose arrangement you like duplicate it just the sheet Then double click on each graph to bring up a dialog where you can choose a different graph for that slot Prism offers a direct way to clone a graph from the Welcome dialog but does not allow cloning of layouts However you can accomplish the
397. t ccceeeececeeeeeeeeeeeeeeeeeeeeeeeeeaeeeeeeseeeeeeeseeeeeeeeaeeeeeesaneeeees 54 Families of Sh 6 ts ii sciis cccececiescecdeenstueeeess ra ainaani aaa haa enaa aaah ENE aeaa tended Aan Enan aa ENUN ces 56 Adding new sheets to your Proje ct cccceeeceeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeseeeeeeenessueeeneneeeees 58 Tips for USING Prism ce cssc ccc cate denceecccces cate Ceuta cgueisaeds det ER EENEN EErEE AARNE cebebesvauesaeeedeestere 59 Differences between Windows and Mac VersiOna ccccceeeeeeeeeceeeeeeeeeeeeeeeeeeeeeeeeeneeeeeees 65 Getting around in Prism 66 Navigator See all sheets in your PrOjeCt cecceeeeeeee cess ence eeeeeeee ee eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeeaes 68 1995 2014 GraphPad Software Inc Contents 3 2 Gallery View all the sheets of one tyPe ececceeeeeeeeeeeeeeeeeeeeeeeeee ea eeeeeeeeeeeeeeeeeeeeeeeeeeeeeeees 69 3 Graph and layout tool tips isciis ccc ciececccesccces coceeencen stteee cceeentaeeeceeus ceaennetessedeenshecnnedeecteenecaaer 70 4 Tools for navigating large Proje cts ccccceeseeeeee esse eeeeeeeeeeeeeeeeeeeeseeeeeeeeeeeeeeeaeeeeeeeeeeeeeeeeees 71 5 Changing the ZOOM sii cciiec ieee cecccess cece ectca din tecetve Headed wedi ENE AEREN EO KEANE AARETE AE AAEE REE nias 74 6 What if the toolbar or navigator iS MISSING ccccceeeceeeeeeeeeeeeeeeeeeeeeeeeeeeaaeeeeeeaaeeeeeeeaeeeeeees 75 7 Opening multiple Prism files ccccceeece cece cece c
398. t File Locations SendtoMS Office View File amp Printer New Graphs Analysis Internet 1 View tab e Set the default fonts for data tables results sheets Info sheets and floating notes e Set the default measurement unit cm or inches e Set Zoom defaults e Set when to show Data and Results folder 1995 2014 GraphPad Software Inc 90 GraphPad Prism User Guide File and Printer tab e Set automatic backup default times e Prism has an option to save files in compact format All this format does is leave out analysis results and instead recomputes them Zipping the file with standard zipping software can do a much better job of compression You also can select an XML Prism format called PZFX as the default for saving all your Prism files This is an XML format that can be opened only by Prism 5 and 6 and not Prism 4 The first part of the file contains all the data tables and info sheets in a plain text XML format that can be viewed by other programs This makes the PZFX format a bit more useful for backups File Format PZF PZF Cannot be opened by Prism 4 but data and info are in XML format that other programs can access Do not save or read page size to or from pef file m Save compact smaller but requires recalculations after opening Z Always prompt when saving to a temporary folder e Choose default way Prism Windows copies files to clipboard EMF WMF or both This cho
399. t Calculate and graph 95 Cl of difference between medians with Mann Whitney test Greenhouse Geisser correction in one way repeated measures ANOVA Ratio t test e Kolmogorov Smirnov test alternative to Mann Whitney Multiple tests one per row with optional correction for multiple comparisons Monte Carlo analyses Multiple comparisons Exact multiplicity adjusted P values with Bonferroni Tukey and Dunnett s tests Graph 95 Cl of difference between means New approach Fisher s unprotected Least Significant Difference LSD New multiple comparisons test Holm Sidak Test main or simple effects after two way ANOVA Dunnett s test now can handle up to 256 groups up from 20 Nonlinear regression Fit to models defined by implicit and differential equations Write more complex models Weight your fit by 1 Y Much easier interpolation Bigger data tables e Create data sets with up to 256 subcolumns up from 52 to Enter data in up to 256 data set columns up from 52 in Prism 5 allow repeated measures 2 way ANOVA with more 1995 2014 GraphPad Software Inc What s new in Prism 6 of Zig zag and elbow lines a ma i ms mic mo Tota 61 mA mes mc mo Tota61 eeeceee Total 61 Pie charts and more Control 1 Hour 6Hours 24 Hours Superimpose individual data points with bars 200 150 100 50 0 Control 1 Hour 6 Hours 24 Hours Superimpose individual data points w
400. t and toolbars to perform tasks 1995 2014 GraphPad Software Inc e GraphPad Prism User Guide 5 1 Navigator See all sheets in your project Each section of a Prism project Data tables Info Sheets Analysis Results Graphs and Layouts can contain up to 500 sheets pages The most versatile way to jump from sheet to sheet is by using the Prism Navigator tree on the left side of the Prism screen The names of all sheets related to the current sheet are shown in bold Click on any sheet name to go there a Family ap Search results s i Data Tables E First try SE Sa ie a i E Areas under curve T Info Method used Si Notes during experiment T Results ob Ea Row stats of First try lex Row stats of Second try ifa Row stats of Third time is the charm flh Graphs o E Second try fie Third time is the charm Le k Summary ih Layouts i For publication i fz For notebook If you need more room to work click the button in the lower left corner of the Prism window to hide the Navigator Click it again to bring the Navigator back See also Tips for navigating large project 1995 2014 GraphPad Software Inc 5 2 Gallery View all the sheets of one type The gallery shows you thumbnails small images of all the sheets in a section at once To view the gallery click on the folder name in the navigator Click on Family Data Table Info Results Graphs or
401. t Graph dialog to change the direction of bars on a graph from vertical to horizontal to set the baseline for graph columns and to adjust the space between columns Double click on any bar to open the dialog 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 255 d Format Graph Appearance Data Sets on Graph Graph Settings Direction Vetical Heeizontal Baseline Automatic Bars begin amp Y Hide baseline Spacing as percent of space used for data Between adjacentdataa 50 X J Additional gap between groups 100 When a value is blank Create a zero heaght bar Don t leave gap Discontinuous axis When the axis is discontinuous ato make the bars or connecting Ines dscontinuou Format of individual bars To format a bar differently than the rest ext thes dialog right cick on the bar and choose Foemat This Bar Flemove all the indvidual formatting Revert all bars to the format of their data set Change Graph Type Hep Cancel Apply 0K 2000 Yetow mo Se 100 1000 ia rT Black Yellow 0 so 1000 1500 2000 2500 You also can use the Rotate button Change Silt ki K Ly fe Baseline Fill in this box to change the baseline for bars on a graph The default is for the bars to begin at the X axis Check the box for Hide Baseline if you want your bars to float as in the example below 1995 2014 GraphPa
402. t click on the sheet name and choose Rename sheet To rename a sheet using the bottom toolbar Click on the sheet name in the bar at the bottom of the Prism window and edit it Don t try to delete the current sheet name from the drop down in the bottom toolbar If you delete the name Prism replaces it with a default name Instead double click on the sheet name in the bottom toolbar to select it and then begin typing to replace it ormalize of Transform of Data 1 graph To change the order of sheets in a section Simply drag and drop within the Navigator or Gallery or pull down the Edit menu and choose Reorder Sheets To delete sheets Select a sheet in the Navigator and click the Delete Sheet s button x on the Sheet toolbar You can select one or more sheets in the current section to delete 1995 2014 GraphPad Software Inc Organizing Prism projects 81 E Delete Sheet s Select one or more sheets to delete Clone of Exponential decay graph Also delete all linked sheets Hint Choose one or more sheets to delete Click to select a sheet click again to deselect it To delete several sheets go to the Gallery and select several sheets Then click the Delete Sheet s button or press the Delete key Because sheets are linked remember that deleting one sheet may affect others When you delete a data table or results sheet you also remove those data and results from all graphs The
403. t for the project L8 GraphPad Prism Project2 Project info 1 i File Edit View Insert Change Arrange Window Help Prism File Sheet Undo Clipboard Analysis Chenge Oraw DB ee 2 ro aa u kid X dtnew e 9 GH S Analyze p Family Consta Value Notes J Search results f J Data Tables Exp niment Date 1 14 2011 H sample excel periment ID 007 Info d Notebook ID 2011 Venice Uh Rest Project Omega il Graphs Experimenter Bond James ke sample excel T Layouts Shaken not stirred How to use Info Sheets To embed all or part of an Info table onto a graph or layout Select all or part of the Info table and copy to the clipboard Then go to a graph or layout and paste This will be a live link updated if you edit the info table Double click on the embedded table to adjust its properties To insert an Info constant into a graph title legend or text object Arrange Draw Write m 8 aie e O T While entering text use the right click menu or click on the Inset Info Constant button in the Write section of the Prism toolbar Prism will maintain a link to the constant updating the text when you edit the info table 1995 2014 GraphPad Software Inc s GraphPad Prism User Guide To change the order of the rows on an Info sheet or to delete a row Click on a row then click the right mouse button From the shortcut menu choose to move the selected row up or down or choose to delete that row Or use the butto
404. t project with a new name We recommend that you backup to the PZFX format rather than PZF because it provides a more secure backup It is possible with some difficulty to extract your data from these files without Prism even if the file is damaged or truncated Recovering files you forgot to save When you exit Prism as with any program it asks you whether you want to save changes to every open file Have you ever clicked No by accident and lost your work Prism 6 saves the file anyway in a special location and keeps it for four days You can open those unsaved files from the Welcome dialog If you delete the file Prism will automatically delete the backup file and not offer to recover it 1995 2014 GraphPad Software Inc Prism files 105 _ If you share a computer with others and don t want your unsaved work to be recoverable you can turn this feature off on the File amp Printer tab of the Preferences dialog Manual backups of Prism data tables You can backup individual data tables using the File Export command You can export to plain text tables delimited with tabs or commas or to an XML format We recommend using XML format even though it is harder to view because it contains more information XML format includes details omitted from the plain text formats including about subcolumns excluded values and floating notes 8 4 Merging and splitting projects Merging Prism offers two approaches to mer
405. t rece cceas vende 419 Navigating a Project visisecsscessscesesscessnteccicevecacesesteusecesencecesneasivevectessespenstseseccetensvenssudtecussbuereaseredentecesevenstvcnectensvers 420 How rows and columns are numbered ccsseeeeeseeeeeeeeeeeeseeeeeeseneesesneeeseneneeseenseeesseeseeesenessesaeneseesneneeeesenennes 421 Adding COMMENES tO a SCIIPt cceeeceeeseeeeseeeeeeeeseeeeeseeensneeesaeeeeseeeesneeesaeeeesaeensaesasaeeeeaeeaseaeesaeeeeseeseseeeeseeeees 421 LOOPS and SIMULATIONS aa rE a aa a a aa a a aaar a aaa aa a a aAa Eae asrdan 422 Creating NEW sheets iienaa aana aaa aa eaaa aa raaa raa aaa aaa raaa aaraa iaa aana aaaeeeaa 423 Changing data table Si r Ee a ae a rae Ea a a A aeaa ra a a Ee aE aaae aeaa aaa aa aa aeiaai 424 Changing graphs ws 424 Setting the default drive and folder cccccceeeceeseceeeeeeeeseeeeseeeesaeeeseeeesseeeeeaeeesaeeeesaeeseaeeesaeeeseseesaeeeseeeeeeeseesas 425 Opening and saving Prism Files c cccescceeseeeeeeceeeeeeeeeeeeseeeesaeeeeaeeesaaeessaeeesaaeeesaeeseaeeeseeeessesessaeeeseeeseeseeas 426 Importing data from a text file ssaseesnueneesnunnnnesnnennnrnnnnnnnnnunnnnnnnnnnnnnnnunnnnnnnnnnunnnnnnnnnnnnnnnnnennnnnnnnnnne nunen anena 427 Importing data from the script file sssanseesneennnnsnuennnesnnennnrnnunnnnnnnnnnunnnnunnnnnnnunnnnnnnnnnnnnnnnnnnnennnnnnnnannn munean nanena 428 COPY ANd Pas C6 E E A A E A TTS 428 Changing info constants j ccscicsssssscerccecces
406. t test data ih Layouts J Floating Note a Date with notes Analyze Data Butan analysis X Which analysis Anahae whch data sets Transform Normalize a JAMae Tarator J B Female Nommeize Pare row Remove baseine and column math Frequency distribution ROC Curve Bland Allman method comparson Correlation Identity outhers Grouped analyses Contingency table analyses Survival analyses Pants of whole analyses Generate curve X ae eae 3 On the first tab of the t test dialog confirm that the experimental design in unpaired and that you want to assume a Gaussian distribution and to perform an unpaired t test For now you can accept all the defaults on the second tab Click the Learn button to read explanations of all the choices 1995 2014 GraphPad Software Inc Parameters t tests and Nonparametric Tests E Expanmental Desg Options E xpermental design Unpared Pared A B of Control Treated d Y res Assume Gaussian distibution Yes Use parametric test No Use nonparametic test Choose test Unpared tert Assume both populations have the same 5D Unpared t test with Welch s comection Do not assume equal SOs Lean Cancel OK 4 View the results Click the analysis checklist button to help interpret the results Click the red properties button if you want to go back to the Parameters dialog to perhaps change to a paired or nonparametric test 1995 201
407. t the name of the second info constant Set the value of the second info constant 0 Set the name of the third info constant Set the value of the third info constant SetInfo Potassium 4 0 Set the name of the fourth info constant SetInfo 3 45 mM 4 1 Set the value of the fourth info constant It would not make sense to create this script by hand but it would be very useful if created by another program 23 1 7 Script example 6 Import data into several tables Script command GoTo D ForEach 9 GoTo N Import Data N txt Next GoTo L 1 Print Comments Go to the data section Loop nine times Go to the Nth data table where N is the loop number Import the data file Data2 txt goes into the second table Data3 txt goes into the third table and so on Loop Go to the first layout which was setup to show all nine graphs Print the layout 1995 2014 GraphPad Software Inc Scripts 23 2 Script syntax Each script command begins with the command name Most commands then have one or several arguments Separate the command name from the arguments with a space and separate the arguments from each other with spaces or commas You can use upper and lower case letters interchangeably and can add extra spaces to improve readability In the rest of this section required arguments are shown in square brackets like this and optional arguments are shown in angled brackets lt like this gt Whe
408. t value greater than the 25th percentile minues 1 5IQR and plot any values that are greater than this as individual points Why 1 5IQR There is no statistical rationale it is simply how Tukey decided to do it and he invented the idea of box and whisker plots Notes on Tukey boxplots e Why 1 5IQR There is no statistical rationale it is simply how Tukey decided to do it and he invented the idea of box and whisker plots e When the Tukey method is used to create the whiskers the ends of the whiskers are sometimes called the inner fences e If the largest value preciesly equals the 75th percentile plus 1 5IQR Prism up to 6 01 and 6 0b does not plot that value as an outlier However if the smallest value preceisly equals the 25th percentile minus 1 5IQR then Prism did plot the point as an outlier We fixed this inconsistency in 6 02 and 6 0c and now do not pot that point individually 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 239 e The values that are plotted individually are sometimes called outliers but outlier is defined differently by Grubbs test or some other outlier test The chance of finding one or more outlier by Tukey s rule in data sampled from a Gaussian distribution depends on sample size If you only enter three values per group n 3 Prism will plot the median and range It will not plot the percentiles and will ignore your choice for how to plot the whiskers Step
409. tJPG command 430 ExpotPCXcommand 430 ExporntPICT command 430 ExpotPNG command 430 ExportTable command 431 ExportTIF command 430 ExportWMF command 430 Be a Families of related sheets 71 Family folder 71 Family of sheets duplicating 93 FAQ tech support 459 Fence inner 237 File compatibility between platforms 43 File formats 100 File locations 89 File locations templates methods examples Files format compatibility 102 Files sending 106 five number summary 237 Flipping transposing a data table Flipping pages Landscape vs portrait 451 355 203 1995 2014 GraphPad Software Inc Index Floating notes 87 Folders of templates methods and example files 451 Font changing Fonts in EPS files Fonts embedding ForEach command Format Axes 273 Format Axis dialog Format Graph dialog Format graph Column Format graph Grouped Format graph XY 213 Fraction of total 357 Frame of graph 273 Freezing a sheet 84 Freezing results 322 Freezing sheets 322 Front to back order of data sets Frozen results 322 FTP 405 Full screen 77 new Gallery printing from 408 Gallery view and choose sheets 69 Gallery working with multiple sheets 81 Gaps inaxis 289 Generate a series of X values Geometric series inserting Getting around 68 Getting started 10 Global changes 192 GoTo command 420 Graph frame 273 Graph legends 369 Graph origin 277 Graph paper making Graph shape 207 Graph size 207 Graph toolti
410. table the connecting lines will jump back and forth across the graph If you want the connecting lines to go from left to right across the graph first sort 1995 2014 GraphPad Software Inc 136 GraphPad Prism User Guide the data table by X values Click on the Sort Rows button on the Change toolbar and sort by X value Cnange Import Uraw OEKD A et wt Sort by X Value Toup Sort by Row Title a Reverse Row Order ta Set Reordering Grouped data Distinguish two ways to reverse order on a Grouped graph Reverse the order of rows Click on the Sort Rows button on the Change toolbar and reverse the order Cnange impon uraw aK A Et aal Sort by X Value iroup A Sort by Row Title ita Set Reverse Row Order This example shows the effect of reversing the order of the rows in the data table 150 150 100 gt 50 50 0 0 ae we 5 S P L E d Reverse the plotting order of data set columns Grouped tables are defined by two grouping variables If you want to reverse the order of how the columns are graphed you don t need to change the data table Instead go to the graph and click the Change data set order button One of the choices on its menu reverses the order of data sets 1995 2014 GraphPad Software Inc Data tables 137 This example shows the effect of reversing the plotting order of data sets Note that this example starts with the same graph as the prior example 150 150 10 9 Changing
411. table has many subcolumns this is the best way to edit column titles X able format This is an XY table Click to ch subcolumn formats or to sho 2 Tite 2 3 z 1995 2014 GraphPad Software Inc Data tables 133 Format Data Table gt a os ame a B U x XOG C Treated with Antagonist Autocomplete Prism uses autocomplete to help you It tries to guess what you are typing and let s you choose from a list of titles you ve used before If you find this more annoying than helpful turn it off in the View tab of the Preferences dialog 10 7 Row titles Why use row titles Row titles have four purposes e Label unknowns in standard curves the labels will propagate through to the standard curve interpolated values results e Label individual points on an XY graph e Label groups in a grouped data table e Label subjects on a column table plotted as a before and after graph 1995 2014 GraphPad Software Inc 134 GraphPad Prism User Guide Show or hide the row title column If you don t see a column for row titles click on the Table format area in the upper left of a data table to open the Format table dialog Choose to Show row titles X Group A G al x ji T 1 271 44 2 51 9 3 56 11 Table format 4 1 Algeria 2 Burkina Faso 3 Burundi Enter two or three line row titles and column titles You may enter two or more lines of
412. tcccee ected veetecdeeccutcueveeadetbeceatieeieestes 28 What s new XY Grap Sae araea sc terenn esrara aro oeann catsseeeseeeacnedarsceessetacesbasrecessciwetentss 30 What s new Grouped graphs secis cciccccesaciieecceuevecestetteecceueesiuspentvecchenveessnenue bewevweesecenver an 32 What s jew Layouts ieena a aaaea aaeeio araia Eanan aeaaea diaa aa seed 33 What was new in Prism 5 sassssnssnsnnunnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnunnnnnnnnnnnnnn nennen nennen 34 How Prism is unique 37 Organized data tabl eS cciicciecseeidscvciaes ruanan i naonn dectasedccnsdaee se eteee deecbschiedeasessencdadvaeetestdserebeers 38 Data analysis for scientists not statistiCiaNS cccceceee eee ee ee cece ee ence eeeeee seen eeeeeaeeeneeeeeees 40 Everything ts Notlinke dsc cece ies ed cove dees Esnea npp eneas teeveicerscouseanedcacsschtcesfeeserataarrbeksedsedentss 41 A complete record of your WOFK cceceeeeeeeeeee eee ee ee ee eeeeeeaeeeeeeeaaeeeeeeaeeeeeesaeeeessaaeeeeeeaaeeeesees 42 Differences between Windows and Mac VersiOna c ccceeeeceeeeeeeeeeeeeeeeeeeeeeeeeeaeeeeneeeenees 43 Getting started with GraphPad Prism 45 A brief tour Of Prisim icccci5 ra a Ee A a aara da a A eceuesdavcecetheevaaeedeys 47 Essential conte pti iiinis a naa deceadedeeesascagechaced ceuetsey tess eeeseeviaatiessaestdeeeedvens 51 Welcome dialog zese dete rerea aae vecees focu E a e aa aA Eear aKo asa 53 The five sections of a Prism PrOjeC
413. te that axis if it doesn t already exist 1995 2014 GraphPad Software Inc 28 GraphPad Prism User Guide lt b RN Na Legend Select Show legend to create a legend for this data set Prism automatically uses the column titles in your data table as legend labels You can also edit the labels in the legend Double click on the legend text and type whatever you like Use the Revert Legend to Column Titles checkbox in the Legend section of the Format Graph dialog to change the labels back to match the column titles This checkbox is only available if you have edited a legend 14 3 2 Data set grouping and spacing on Grouped graphs How do you change the grouping and spacing of bars on Grouped graphs Click on the Format graph button on the Prism toolbar or double click on any data point to open the Format Graph dialog Change fi E de K u s amp Set the standard spacing between bars To change the standard spacing between individual bars and groups of bars go to the Graph Settings tab 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 249 FFomast Graph Appearance Data Sets on Graph Graph Settings Direction Vertical Heeizontal Baseline Spacing as percent of space used for data Between adjacent dta 50 X ditional gap belween groups When a value is blank Create a zero heaght bar Don t leave a gap Discontinuous axis hen the axi
414. tencies between the English version and any translations 25 6 Training If you would like an on site course in using GraphPad Prism we recommend that you contact Star Training Service Jimmy Walker has presented courses in Prism to pharmaceutical companies around the world and receives rave reviews His courses are informative and fun and appeal to both new and experienced users Email jimmy startrain com or call 415 893 1835 or fax 415 893 9196 Star Training Service is completely independent of GraphPad Software 1995 2014 GraphPad Software Inc 468 GraphPad Prism User Guide 1995 2014 GraphPad Software Inc tes E Index 5 5 number summary 237 A Adding a new data table 122 Adding comments to a script 421 Adding data to graph 195 Adding pictures 376 Adding text 371 Adding text with Word 374 Additional gridlines 292 Additional ticks 292 Aligning objects 379 Alignment guides 379 alpha channel 389 Analysis chains 71 Analysis constants hooking 326 Analysis parameters 321 Analyze dialog 318 Analyzing data analysis constants 326 Analyzing data chaining analyses 320 Analyzing data changing inputs and choices 321 Angled text problem with Mac 404 Annotating graphs and layouts 87 Annotating graphs and layouts highlighting 88 Annotating graphs and layouts lines and boxes AffPotating graphs and layouts text 371 Antilog transform 348 AppleScript 441 Apply button 192 194 ApplyColorS
415. the Data and Results folder or to show it always even when you haven t created any analysis chains These choices are in the View tab of the Preferences dialog 1995 2014 GraphPad Software Inc Analyzing data with Prism 321 16 3 Changing an analysis After reviewing the results of an analysis you may want to change your choices Click on the Results button in the upper left corner of any analysis results sheet to open the Analysis Parameters dialog P GraphPad Prism dose response pzf Nonlin fit of Normalize of Transform of Dose response data experiment 1 amp File Edit View Insert Change Arrange Window Heip Prism File Sheet Undo Clipboard Analyses Interpret Change Draw Write Text hm O B 2e2x o XG SP a X nwe 9e D Anayze Fy Ey a a BJU Xx m a Family Search results a i Data with Results B J inhibitor 1 10 gt p Dose response data experimei a r Seana L Normalize of Transform 5 Conclusion alpha 0 05 Nonlin fit of Normalize 6 Preferred model I Table of results 7 F OF n DFd I Curve ji s karri 9 LogEC50 different for each data setl Project info dose response experit Best fit values m Results Bottom ii Graphs op kd ec50 dose response Ary Layouts Layout 1 I Floating Notes Two buttons in the toolbar let you change an analysis pn Change the analysis parameters choices Change which data table and data sets are analyzed 1995 20
416. the Import and Paste Special dialog where you can unlink the values if you want to Group A Group B Data Set B Data Set A 10 Prove to yourself that the values are linked Change the data being analyzed and notice that the summary values that you paste linked automatically update 11 Create a graph of these values using New Graph of existing data 12 Compare the groups of values with a test 1995 2014 GraphPad Software Inc 162 GraphPad Prism User Guide 13 Download the Prism file Example 2 You have two sets of column data that you wish to plot both as a bar graph showing the mean and SD and also has a scatter graph showing individual values One approach is to superimpose the bars and individual symbols Prism 6 makes this simple as it offers this as one of the choices for column graphs This can look good if you omit the error bar but looks cluttered when you include error bars I used light colors for the symbols in the graph below which helped a bit 150 gt 100 E 2 50 0 Pa e we Another approach is to put the bars and symbols side by side Follow these steps 1 Enter the two columns of data into columns B and C 2 Select the values in Column B and copy to the clipboard 3 Put the insertion point at the top of column A and choose Paste Link from the Edit menu or the right click shortcut menu 4 Select the values in Column C and copy to the clipboard 5
417. the data table empty Prism automatically figures out what to do with missing values When Prism imports a text file it handles missing values automatically Some other programs use a code say 99 to denote missing values If you import data from such a program enter that code value into the Filter tab To denote an excluded value in a text file or within Excel put an asterisk immediately after the value Then check the option on the Filter tab to exclude values followed by asterisks Pick which Rows you wish to import or skip First select the range of rows to import by specifying a first and last row If the file you are importing includes lt notes gt lt info gt or lt title gt information see Paste Special Notes start counting rows at the first row after this structured information Row 1 is the first row with data not the first row in the file Then select rows you want to skip The filters work by checking whether a designated column meets a criterion you specify You can apply any combination of 1995 2014 GraphPad Software Inc GraphPad Prism User Guide three kinds of filters Skip all rows until a criterion is met Skip all rows after a criterion is met Skip every row that meets your criterion When defining the criterion you can use any column in the original file You are not restricted to using columns you choose to import Compare by checking whether the value of each row in the column is less t
418. the results information and this grid lines will update 15 2 8 Axis titles By default Prism puts generic titles on top of the graph and on the X and Y axes To edit a title Click in the title to select it If you are editing a Y axis title it will be temporarily displayed horizontally for editing Edit or replace the text To enter more than one line press Enter between lines When you are done click in the background of the graph While editing the title you can use controls in the text toolbar 1 xr 14 v Arial A A A B I U X2x To delete a title Drag over the title to select it If you are editing a Y axis vertical title it will be temporarily displayed horizontally for editing Then press the DEL key To bring back a deleted title Double click an axis to open the Format Axes dialog Check Show title in the Titles and Fonts tab of Format Axes dialog To change the font of a title Select the title or a portion of it and use Font tools on the toolbar Or double click on the axis to open the Format Axes dialog go to the Titles amp Fonts tab and click the Font button To make a title a bit smaller or bigger Select the title Then press the A or buttons on the toolbar to change the point size To justify a title Usually a title is centered over the graph or axis To justify the title with the right or left edge of the axis select the title and click on the text justify button on the Text
419. the subjects only had data for three time points with the fourth time point missing Linear and nonlinear regression Fitting lines and curves works fine with missing values You can choose whether Prism fits the individual replicates or fits the means If you choose to fit the means each mean gets the same weight regardless of how many values were used to compute it If you fit the individual replicates then X values with more Y replicates get more weight than X values with fewer replicates Survival curves Comparison of survival curves does not require equal sample size If data are completely missing for any subject simply don t enter data for that subject But before deciding to leave data out read about censoring which happens when you know the subject survived up until a certain time but don t know what happened after that or you know but can t use the data because the experimental protocol wasn t followed Prism handles censored data fine Don t omit those subjects enter the duration that they survived on the experimental protocol and mark that duration as censored 10 13 Keyboard shortcuts e The Tab key moves to the right Shift tab moves to the left e The Enter key moves to the right to the next subcolumn if there is one otherwise it moves down a row and to the first subcolumn Shift Enter does the opposite e The DEL key erases all selected values but the data set will still be linked to analyses and graphs
420. then start over An alternative approach is to change the region linked within Prism Click on the linked data object then pull down the Edit menu and choose Links pe Links amp Oe _ noe Links Type Update Cancel Update Now 0 a Change Source Break Link Source C _ iles sample excel sds Sheet 1 R4C1 R17C2 Type Microsoft Excel Worksheet Update Atomatic Manual You will see a list of each linked data range on the current Prism table with the region you selected already highlighted Press Change Source to bring up a second dialog 1995 2014 GraphPad Software Inc Importing and exporting data 185 At the bottom of that dialog you ll see the current linked range in the field labeled Item Name With Excel this range is formatted in an unfamiliar way R1C3 R100C4 goes from the first row of column 3 to the 100th row of column 4 Note that you can also use this dialog to link to a different Excel file To change the region of a spreadsheet embedded within Prism Windows only If you accidentally embedded the wrong part of a spreadsheet you ll need to copy and paste again You can t simply delete the data object and start again because the object contains the embedded Excel table If you don t have the original spreadsheet file you need to save it from Prism To do this open the embedded spreadsheet from Prism and then use Excel s File Save Copy As command to save the spreadsheet a
421. these portfolio graphs are linked to step by step instructions Others give brief explanations Exploring these files will help you master graphing with Prism 2 What s new in Prism 6 When creating Prism 6 our goals were ambitious e To simplify Prism so it is easier to learn and even more efficient to use e To greatly improve its statistical clout and graphical versatility e TO make Prism 6 appeal to a wider group of scientists and students e To make the transition from Prism 5 or earlier to Prism 6 be graceful and for people who make the switch to rapidly discover that Prism 6 simply works better Links to the full lists of new features Highlights Statistics Multiple comparisons Regression Data tables Working with other programs Parts of whole data Column graphs XY_Graphs Grouped graphs Layouts Time savers 1995 2014 GraphPad Software Inc What s new Highlights Prism 6 is a big upgrade with many improvements It has more statistical clout can make more kinds of graphs and is even more efficient to use But Prism is still Prism The basic interface and organization of the program has not changed so you can switch to Prism 6 with almost no learning curve And you can try the Prism 6 demo without removing Prism 5 Statistics Two way ANOVA with repeated measures in both factors Detect outliers in a column of data using Grubbs test Calculate and graph 95 Cl of median with Wilcoxon tes
422. tibitor 2 Best fit values ae Std Error ES Lower 95 confidence link 2 8 Upper 95 confidence link gy Dependency i 8 Goodness of Fit fB inhibtor 1 10 i EE Best fit values H a Std Eno gy Lower 95 confidence link Upper 95 confidence lint Dependency Goodness of Fit w 6 ff Global shared 1995 2014 GraphPad Software Inc Simulating data and Monte Carlo simulations 335 17 Simulating data and Monte Carlo simulations Simulating data is a powerful way to understand statistical analyses and plan experiments Monte Carlo analysis lets you simulate many data sets analyze each and then look at the distribution of parameters results of those analyses This can let you experiment with alternative experimental 1995 2014 GraphPad Software Inc 33 GraphPad Prism User Guide designs via computer before you collect any data Prism makes it easy without requiring any programming or scripting 17 1 Simulating a data table To simulate a family of XY data sets with random error start from any data table or graph click Analyze open the Simulate data category and then select Simulate XY Data 1995 2014 GraphPad Software Inc Simulating data and Monte Carlo simulations 337 X values tab Generate a regular series arithmetic or geometric of X values or use the X values from the data table you are analyzing Equation tab You can choose to use Y values from the data table you are analyzin
423. ting rows 356 Default preferences 89 Del key shortcut 142 DeleteAllDataSets command 424 Deleting data from graph 195 Deleting sheets 80 Depth charts 366 Dictated notes 87 Directories of templates methods and example files 451 Discontinuous axis 289 Displays using two 76 donut charts 266 Dragging graph to layout 363 Drawing 375 Duplicate family 93 DuplicateDataTable command 423 DuplicateFamily command 423 Duplicating a data table 122 Fa Electronic notebook 107 ELN 107 Emailing files 106 Embedding and linking data 160 Embedding and linking data objects 172 Embedding fonts 392 Embedding results 325 Embellishing a graph 375 EMF or WMF format 399 EMF vs WMF 89 EMF exporting 384 1995 2014 GraphPad Software Inc EndTable command 432 Enter key shortcut 142 EPS files and fonts 392 EPS exporting 384 Equations adding to graph 376 Equations adding your own set Error bars on Column graphs Error bars on Grouped graphs Error bars on survival graphs Error bars on XY graphs 147 Example graphs 94 Examples saving in a lab Examples scripting 413 Excel files importing 169 Excel working with Mac 165 Excel working with Windows Exchanging X and Y values Excluding outliers 139 Excluding values 139 Export graphs and layouts ExportBMP command 430 ExportEPS command 430 Exporting graphs and layouts Exporting multiple sheets 81 454 150 150 153 451 163 348 355 384 397 Expon
424. tion of parameters in models of ligand receptor interaction to log or not to log Trends in Pharmacological Sciences Volume 19 Issue 9 1 September 1998 Pages 351 357 Prism file for this example Using a script to simulate many data sets This page will help people who set up these scripts in earlier versions of Prism or people for whom the Monte Carlo analysis doesn t provide enough versatility But for most people the Monte Carlo analysis will be much easier Follow these steps 1 Create a Prism project that simulates a data set with random scatter the first results sheet and then fits a curve through these data with nonlinear regression second results sheet 2 Make sure that the first data table is empty and formatted for column data no X column no Y subcolumns The script will write the results into this table You can click in the upper left corner of the data table to change its format if needed 3 Click the Prism button at the left of the toolbar and choose Run Script Then choose New Script and start with a blank page 4 Enter this script Table Prism 1 Clear Foreach 100 Goto R 1 Regenerate Goto R 2 WTable logEC50 5 1 Next 1995 2014 GraphPad Software Inc Simulating data and Monte Carlo simulations 343 5 Click the Run button on the Script dialog 6 After the script is complete go to the first data table and view the results 7 Click analyze and choose to do Column statistics
425. tions lt ren ele ele Navigate within sheets in a family 1995 2014 GraphPad Software Inc GraphPad Prism User Guide At the top of the Navigator tree there is a section that organizes related sheets as Families When you select a sheet in any section of the Navigator all the related sheets data tables graphs info sheets results and layouts will be grouped and shown in the Family section CD Family of Normalize of Trar E Data 1 f Transform of Data 1 g Normalize of Transform L4 Nonlin fit of Normalize lA Table of results l Curve l Normalize of Transform Search results Data with Results Data Tables m Mos 1 This folder is especially useful when working with a project with lots of sheets It lets you move between related sheets without scrolling the Navigator The keyboard shortcut to open the Families folder is Ctrl L Use the link button on the bottom toolbar to move between sheets in a family Note below that each type of sheet is marked either D for data table R for results and G for Graph _ Not R Transform of Data 1 R Nonlin fit of Transform of Data 1 R Normalize of Transform of Data 1 R Nonlin fit of Normalize of Transform of Data 1 G Data 1 graph G Transform of Data 1 graph G Normalize of Transform of Data 1 graph L Layout 1 Working with chained analyses Prism lets you chain analyses For
426. to equalize all graphs on the layout 2 Choose Equalize Scaling Factor from the Arrange menu or press the button in the Change section of the toolbar amp 3 Choose to reduce the scaling factor of graphs that are larger than the others or to increase the scaling factor of those that are too small If graphs were originally made the same size with same size fonts this command will get things the same again on layout If graphs started off with different sizes however this command won t be very helpful 1995 2014 GraphPad Software Inc 366 GraphPad Prism User Guide Equalize Scaling Factors x Deane ie ee Size on Layout ennition of scaling factor Size in Graphs Equalize the scaling factor of All graphs on the layout Selected graphs only f Change the scaling factor to Reduce scaling factors to match the smallest 113 Increase scaling factors to match the largest 122 Set all scaling factorsto 100 Fe Increase or decrease the scaling factor of all graphs full 1 Choose Resize Layout from the Change menu or click the Resize button i 2 You ll see a menu with choices Smaller Larger To Fill Page or More Choices which brings up the dialog shown below Resize Layout s Resize the entire layout O To 100 of ts current size As large as possible Make the layout width 1035 in Y Change point size of text proportionally Move to Q Center of poge
427. trol Data on graph al Sample column data B Drug A Add Sample column data C Drug B Sample column data D Drug A B _ Replace Remove Reorder Top Reverse Down Bottoen pace between selected data set and the previous on 100 of normal Note one possible source of confusion When you enter a value here as the space between a selected data set and the prior one you enter the percentage of the gap set in the Graph Settings tab If you enter 200 you are setting the gap between the selected data set and the prior one to be twice as large as the usual gap When you enter a value on the graph settings tab as space between columns enter the percentage of the width of the bar or plotting area for the set of scatter symbols A value of 50 means the gaps between bars are half as wide as the width of the bars Adding a line between adjacent columns 1995 2014 GraphPad Software Inc 232 GraphPad Prism User Guide 150 100 v v ai S Wy To add a line between two adjacent bars go to the Data Sets on Graph tab Select a data set and enter at the bottom of the dialog the specifications of the line you desire Appearance Data Sets on Graph Graph Settings Data sets plotted left to right cy Sample column data A Cortrol HERE Sample column Between selected data set and the previous one 100 2 F Separate this data set from the prior one wit
428. ts 105 Commands scripting 420 Comments addiing toa script 421 Compatibility between Prism and other programs 102 Compatibility between Prism versions 102 Compatibility of files between platforms 43 Compatibility Windows and Mac 43 Compressed format 100 Constants hooking analysis constants 326 Contingency data tables 117 Contract 462 Control space shortcut 142 Copy and paste 399 Copy command 428 Copying between projects 105 Copying problems 89 Courses inPrism 467 Create series 143 Createlog command 438 CSV files importing 168 Ctrl key shortcut 142 Ctrl space shortcut 142 Custom ticks 292 D Data analysis 320 321 Data objects changing 183 Data objects creating 172 Data sets on graph 195 Data table decimal places 138 Data tables changing the format 122 Data tables Column 115 Data tables Contingency 117 Data tables Grouped 116 Data tables Parts of whole 119 Data tables starting or duplicating 122 Data tables Survival 118 Data tables Which one for a bar graph 124 Data tables XY 113 Data tables vs projects 122 Data tables column titles 131 Data tables excluding values 139 Data tables key concepts 109 Data tables printing 408 Data tables row titles 133 Data tables sorting 135 Data pasting from Excel Mac 165 Data pasting from Excel Windows 163 Data pasting from text files 168 Data results folder 71 Decimal places 138 Decimals rounding 145 Decima
429. ts has no other meaning The blue dots represent a data set where each value represents a Y value 1 5 times higher than the one below On the graph on the left the lower values are almost superimposed making it very hard to see the distribution of values even with horizontal jittering On the graph on the right with a logarithmic axis the points appear equally spaced Why logarithmic In the example above the ticks at 1 10 100 1000 are equally spaced on the graph The logarithms of 1 10 100 and 1000 are O 1 2 3 which are equally spaced values Since values that are equally spaced on the graph have logarithms that are equally spaced numerically this kind of axis is called a 1995 2014 GraphPad Software Inc 304 GraphPad Prism User Guide logarithmic axis Interpolating between log ticks What value is halfway between the tick for 10 and the one for 100 ona logarithmic axis Your first guess might be the average of those two values 55 But that is wrong Values are not equally spaced on a logarithmic axis The logarithm of 10 is 1 0 and the logarithm of 100 is 2 0 so the logarithm of the midpoint is 1 5 What value has a logarithm of 1 5 The answer is 101 5 which is 31 62 So the value half way between 10 and 100 ona logarithmic axis is 31 62 Similarly the value halfway between 100 and 1000 on a logarithmic axis is 316 2 Lingo The term semilog is used to refer to a graph where one axis is logarit
430. tting order of Column graphs Additional Column graph settings Replicates and error bars on Column graphs 14 2 1 Appearance of Column graphs Format Graph dialog Column graphs Use this dialog to change the look of all the columns in a data set If you want 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 225 to change the look of a single column use the right click menu You can also change all the symbols in selected data sets Double click on any graph symbol or bar to open the Format Graph dialog r Format Graph Appearance Data Sets on Graph Graph Settings Data set Entering eroe values computed elsewhere Treated Global Style Appearance Bar X Piet Mean with SD X Bars and boxes Fi Patter i Pattem color aaa Border 2 pt Border color i Symbols Color ZZ SS Error bars Coke MMMM Sye T Dit Above Thickness 2pt Lines peo Additional options Plot on Left Y axis Show legend Revert legend to column tit Right Y axis abel each port with it Change Graph Type Help Cancel Apply OK To change the settings for one data set Select a data set from the list and choose the bar format and fill lines and error bars for that data set Then select another data set and choose settings for that data set Click OK to redraw the graph with all the changes Note that a fitted curve is treated as a separate data set
431. tton in the Prism toolbar and click the Gallery option in the Print dialog 23 Scripts 1995 2014 GraphPad Software Inc n GraphPad Prism User Guide Use a Prism script to automate the analysis of a large number of files Prism s scripting language lets you open and close Prism files import data and export or print results and graphs 1995 2014 GraphPad Software Inc 23 1 Example scripts The easiest way to learn Prism s scripting language is to follow some examples The examples are all for Prism Windows The only difference on a Macintosh is that you use a colon instead of a backslash to specify disk names folder names and files For example the first line of the first example would read SetPath Hard Drive Prism 4 Data June21 Script example 1 Repeatedly import data Script example 2 Monte Carlo analysis Script example 3 Import several files onto one table Script example 4 Open a template and import data Script example 5 Import data and info constants fromthe script file Script example 6 Import data into several tables 23 1 1 Key concept What is a Prism script Because Prism links data to graphs and analyses a great deal of automation is built in Simply edit or replace data or info constants and everything will be updated Although this built in automation suffices for day to day lab work it can be tedious when repeated over and over You can use a Prism script to automate the analysi
432. uble click on an axis to open the Frame and Origin tab of the Format Axes dialog Or click on the Format Axis tool in the Prism toolbar Choose to hide one or both axes in the Frame amp Origin section You can also choose to Show Scale Bars 1995 2014 GraphPad Software Inc GraphPad Prism User Guide Format Axes Frame and Origin X axis Left Y axis Right Y ais Titles amp Fonts Origin Set origr Automatically X Y intersects the X ais amp X X intersects the Y ass at Y Shape Size and Position Size Wide Distance of Y axis from left edge 275 in Width Length of X ais 3 00 in Distance of axis fram bottom edge 4 43 in Height Length of Y axis 200 in Axes and Colors Thickness of axes 1p X Color of plotting area Clear xj Color of axes ia Page background _ Ow x Frame and Grid Line Hide axes Major git Hide Y ShowX None Hide both X and Y Color Show both X and Y Y Thickness 2 pt var Style Style Scale bars To show or hide the scale bar If you choose to hide either axis a new option will appear in the Frames and axes section of the Format Axes dialog Show Scale Bar Check this option to see scale bars uncheck to hide scale bars The length of the scale bar equals one axis interval set in the Regularly Spaced Ticks section of the Format Axes dialog To delete a scale bar Click on a scale bar to select it and then press DEL to delete it To chang
433. ubset of data sets Changes you make after that will then apply to all selected data sets Global There is a shortcut for changing all Hold down the control key Note the globe cursor since you are making global changes Style Choose how to plot error bars Select SD SEM 95 CI or range If you created a data table with no Y subcolumns you won t have any choices here But if you entered data into subcolumns the choices here determine how the replicates or error bars will appear The Appearance drop down on the left determines the basic look with further choices in the Plot drop down to the right the choices will depend on what you select in Appearance Format Graph re Appearance Date Sets on Graph Graph Settings Date set form of Dose response data experiment Tino inhibtor lt gt Global m d o J Show symbD Mean ory Mean and Error Colo MB Median only a Median and Error Ber Each Replicate Show bars spikes droplines 30 20 25 25 20 20 15 16 10 10 s 5 o 0 or oe oe ee oe Since it rarely makes sense to choose different error bar or replicate choices for different data sets you will probably want to click Global and then All before changing error bar format Show symbols 1995 2014 GraphPad Software Inc Graphs Symbols bars lines and legends 215 Choose symbol type size and color If you pick an open symbol also select a border thickness Check
434. um Three segments 4 H l Maximum All ticks Set the range of each segment and its length as a percent of the total length of the axis 1995 2014 GraphPad Software Inc 200 GraphPad Prism User Guide Format Axes Frame and Origin x axis Left Y axis Right Y axis Tiles amp Fonts Gaps and Direction Two segments b X Scale Segment ED Range Bottom Top Lengtk 50 of axis Minimum 0 07 Finally choose the spacing and properties of minor and major ticks separately for each axis segment Adjusting the position of the gap on the graph To move the gap along the axis or make the graph wider or narrower click on ab axis segment to select it and then e Drag the knob just to the left of or below the gap to change the position of the gap along the axis make one segment larger and another smaller e Drag the knob to the right of or above the gap to widen or narrow the gap itself Example 1 Activity 75 50 25 3 ee ai mmama ee ee ee ee ee ee a ee ee ee ee 0 5 10 15 20 30 40 50 Minutes e Left segment range O to 15 e Left segment length 67 of the total e Right segment range 15 to 50 e Right segment length 33 of the total 1995 2014 GraphPad Software Inc Graphs Frame and axes 291 Because of the change in scale the linear regression line appears to have two Slopes In fact the mathematical slope is identical everywhere and the line was c
435. umber of rows 7 11 9 8 s pecified rows in that order Columns The parameter for columns can designate a single column a column across until an empty column a range of columns or a list of columns which can be in any order You must have used the OpenOutput script command first to specify where the results will be written Whatyou Mow Prism Interprets it enter E column 3 The column of row titles if it exists is column 0 Column 1 is column A 3 but for some results there are no A B C column labels 33 Only column 3 The column with titles is 0 so in the example above this is the significant column 3 On column 3 3 Stat at column 3 and keep going right until a column is empty or the end of the table 3 4 Columns 3 and 4 3 6 Columns 3 4 5 and 6 Columns 3 then 8 then 4 Note that the order in the results will not match the order in ana the Prism table Also note that included spaces after the commas which are ignored 3 84 1995 2014 GraphPad Software Inc 436 GraphPad Prism User Guide Row label The parameter row label would must be quoted text That text will appear as the first item in every row output If the WBlock command ends with a semicolon then there is no delimeter no tab no space no comma after that text If there is no semicolon then the row label text is separated from the next column just like all the columns are sepa
436. umn O refers to the X column and column 1 is the first Y column column A You can also write out entire rows or columns or the entire sheet at once The commands that begin with WT transpose the data so each row becomes a column before writing to the text file WVersion writes the version of Prism you are using to fully document your results Note that the WTable command is distinct from the set of commands described here despite the fact that it begins with the letter W Read more about WBlock and WTBlock 1995 2014 GraphPad Software Inc 23 2 18 The WBlock and WTBlock commands These commands will be introduced in GraphPad Prism 6 04 and 6 0e The idea is to specify a block range of cells to write to a text file already specified in an OpenOutput command WBlock script command Syntax WBlock row s column s lt row label gt lt gt Rows The parameter for rows can designate a single row a row down to a blank row a range of rows ora list of rows which can be in any order You must have used the OpenOutput script command first to specify where the results will be written What you How Prism interprets it enter 7 Only row 7 Of course row 7 is the row labeled with a 7 in front of it so row 0 is the column titles Too Onyow S O 17 Stat at row 7 and keep going until you hit a blank row 7499 Start at row 7 and end at row 12 Note that the second number is the ending row not the n
437. ur equation and clicks Details they will see a small preview Of the graph that is linked to the equation Make sure this graph is easy to comprehend at small sizes 4 When entering each equation also consider entering a description and tip The tip appears on the Fit tab of nonlinear regression The description appears on the Details page 5 Save the file to the Equations folder within the Prism program folder Use a name something like this Smith Lab Flow cytometry equations so it is very clear to anyone using Prism that these equations did not come from GraphPad we won t be able to answer questions about them Please do not delete any equation files that came with Prism 6 Quit Prism then restart it You ll now see your list of equations in the Fit tab Of nonlinear regression 1995 2014 GraphPad Software Inc Standardizing Prism use in a lab as 7 If you need to edit your file move it out of the Equations folder and restart Prism and edit Save your changes quit Prism move the file back to the Equations folder and restart Prism You might notice this folder containing pze files C Documents and Settings All Users Application Data GraphPad Software Pri You don t need to manage this folder These are files that Prism creates in order to load equations more quickly It will automatically create or update the needed file if you add or modify an equation file as detailed above 24 5 Using a local
438. ur raw data alone and places the calculated values on results tables You ll never confuse raw data with calculated results You ll never wonder how values were computed 3 921 3 947 3 729 3 766 3 798 3 898 3 945 3 938 3 714 3 611 3 499 3 870 3 812 3 55 3 626 3 928 Data analysis for scientists not statisticians Understandable analysis dialogs Prism presents analysis choices in clear language and avoids statistical jargon Statistical help when you need it r Parameters t tests and Nonparametric Tests Experimental Design Options Experimental design Unpared Pared A 6 Control Treated rf 4 R lt Assume Gaussian distribution Yes Use pxametic test No Use nonparamene test 1995 2014 GraphPad Software Inc How Prism is unique a C onsu It Pris m s com p re he ns ive Prism offers seven related tests that compare two groups To choose among these tests answer three questions in the Experimental Design tab of the t test parameters dialog O nline help to review the basic Experimental design unpaired or paired p rinc iples 0 f data a na lys is a nd Choose a paired test when the columns of data are matched That means that values on the same row s are related to each other to understand your analysis Here are some examples cho ices You measure a variable in each subject before and after an intervention You
439. use as constants as lt Info gt e Mark sections you want to go into the freeform Notes areas of an Info Sheet as lt Notes gt e Mark a section to use as a title for your Info sheet as lt Title gt Example lt Info gt Experimenter Dave Jones Lot number 564A 1995 2014 GraphPad Software Inc Importing and exporting data as Specific radioactivity 345 6 lt Info gt lt Notes gt Th xperiment went smoothly but we noticed a large bubble in the thir lt Notes gt lt Title gt Experiment of June 32 2098 lt Title gt Enter a tab after the lt Info gt variable name to separate it from its value If the variable name is two words use quotation marks around the name The three blocks info notes and title can appear in any order but they must appear at the beginning of the file You can include one two or all three of the blocks If the info variable already exists its value will be updated If the variable doesn t exist it will be appended to the Info table Notes will be appended to the notes right portion of the Info sheet It is not possible to include Greek letters or super or subscripts when importing The title you enter if you include a lt title gt section will replace the data table sheet title When you use the View tab to preview your data the preview will not include the structured information enclosed in notes info or title tags Wh
440. user Library Preferences com GraphPad Prism plist With older versions of OSX you can locate the file using Finder and drag it to the trash With Lion the file is invisible To delete it launch the Terminal application and enter this command rm Library Preferences com GraphPad Prism plist How to prevent saving changes to the preferences file Windows When Prism is used in a teaching lab you want Prism to startup the same way each time When a student uses Prism you don t want preferences set by other students to be used as that would make it seem that Prism acts unpredictably The first step is to create and write protect the preference file 1 Delete the Prism preference file Prism6 cfg from 1995 2014 GraphPad Software Inc aso GraphPad Prism User Guide system disk Users user AppData Roaming GraphPad Software Prism 6 0 2 Launch Prism so it creates a default preference file 3 Set any preferences as you want them to appear for each user 4 Create any color schemes you want everyone to have access to as well as user defined equations you want everyone to access 5 Quit Prism Now the preference file is saved 6 You might wish to write protect the preference file to make sure it isn t changed in the future The second step is to add C to the Prism command line to tell Prism not to resave the preference file when it exits Individual users will still be able to make changes to the Preference file an
441. users also create a web htm file that explains use of the template or method Give it the same name as the template or method but with the extension htm and place it in the same folder For example if your template is doseresponse pzt create a help file named doseresponse htm When someone uses the template or method Prism will pop up the dialog with the brief instructions This dialog also has a button Help for this template When your uses click this button Prism will launch a web browser to display the htm file you created 1995 2014 GraphPad Software Inc as GraphPad Prism User Guide 24 4 Adding your own built in equations Prism makes it easy to add your own equations and these will appear in the User defined equations group of equations But if you want to share a set of user defined equations with others in your lab you can create a new group of equations that will appear underneath the ones we provide To add a new group folder of equations create a Prism file and place it in the appropriate spot 1 Start a new Prism project Go to preferences file and printer tab and make sure that you are saving in pzf format and that the Save compact option is not checked 2 For each equation either fit a data set with nonlinear regression or simulate a theoretical curve plot a function Reorder the results pages to the order you want the equations displayed in the equation list 3 If a user picks yo
442. ve the graph on a page or stretch its axes e Instantly switch between black and white colors and shades of gray You can bring up the color scheme dialog if you want to choose among many color schemes But Prism 6 makes it super fast to switch between color and black and white includes shades of gray Change Arrange Draw nie Mik a E GQ n vais Kibet amp O THO AaB Black and White f Colors More Color Schemes Set the Default Color Scheme Background gt Plotting Area Axes gt Easier to navigate around Prism e Search for sheets Prism lets you organize projects the way you want to with no limit to the number of sheets that a project can contain But if you put hundreds of sheets into one file you may have trouble finding the sheet you need Prism 6 lets you search within a project to find all sheets that include the specified text e More galleries Prism 5 lets you view all graphs at once ona gallery Ditto for data tables info tables analysis results and layouts Prism 6 also lets you view 1995 2014 GraphPad Software Inc What s new in Prism 6 23 an entire family of linked sheets in the gallery or to see the entire set of search results See above as a gallery e Crisper on screen graphics We ve revamped how Prism Windows handles onscreen graphics It won t affect how your graphs look when exported or printed but graphs look much crisper on screen in Prism 6 New choices in the Welcome
443. ver Drop the File menu and choose Post to Web and choose to send the current sheet all graphs or all layouts Prism will post the graphs or layouts on your FTP server and create an index page Immediately after posting the graphs Prism will launch your browser and take you to that page Copy the URL of the created page and email it to others so they can view your graphs Note that Prism posts only pictures of your graphs or layouts for others to view It does not upload the Prism file itself Specifying the FTP server Before you can post to a Web site or FTP server you must configure Prism to do so Drop the Edit menu Prism menu if you use Mac OS X choose Preferences and then choose the Post to Web tab This dialog also will come up the first time you click on the Post to a Web site button in the Send section of the Prism toolbar 1995 2014 GraphPad Software Inc s GraphPad Prism User Guide r Preferences InfoSheet File Locations Sendto MS Office View File amp Printer NewGraphs Analysis Internet Prism makes it really easy to post graphs and layouts to the web You can then email the URL to colleagues who will be able to view your work Your colleagues will need only a web browser to view your graphs and will not need GraphPad Prism Before you can post for the first time you need to tel Prism where pou wart to post To do thes you need to enter pour FTP account nfo on this scr
444. vew 174 Pasting data from Excel Mac 165 Pasting data from Excel Windows 163 Pasting data from files 168 PCX importing 376 PDF exporting 384 Percentage of total 357 432 433 473 GraphPad Prism User Guide Phone support why we don t offer 459 PICT exporting 384 PICT importing 376 Pictures importing 376 pie charts 266 Ping pong button 71 Placeholders on layouts 360 Placing a graph in a layout 362 Platform differences between Windows and Mac 43 PNG exporting 384 PNG importing 376 Pointers 59 Portrait vs landscape 203 Portrait vs landscape Graphs 409 Portrait vs landscape Tables 408 Positioning 379 Posters 362 Posters printing 409 PowerPoint 399 PowerPoint sending to 89 PowerPoint One click export to 397 Precision rounding errors 145 Preferences 89 Print buttons 408 Printcommand 420 Print vs Quick print 408 Printing datatables 408 Printing multiple sheets 81 Printing Landscape vs portrait Graphs Printing Landscape vs portrait Tables Prism 3 compatibility with 102 Prism 4 compatibility with 102 Prism gallery view and choose sheets 69 Prism Gallery working with multiple sheets 81 Prism Magic Make graphs consistent 197 Prism Navigator 68 Problems with copying and pasting 89 Process colors 391 409 408 Programming Prism Scripts 413 Projects vs data tables 122 Projects merging and splitting 105 Pruning rows 356 Publishing 384 Publishing to Web PZ
445. vival Parts of whole One way ANOVA Ordinary One way ANOVA Repeated measures ROC curve More sample data sets x Open a file LabArchives Clone a graph Graph portfolio Prism Tips Cancel Create 1995 2014 GraphPad Software Inc How to learn Prism 11 The data table with sample data also contains a floating note that explains how the data are arranged and gives suggestions for graphing and analyzing Follow step by step examples using sample data for analyzing data with Prism Descriptive statistics Column statistics Frequency distribution Compare two groups Unpaired t test from raw data Paired t test Mann Whitney test Wilcoxon matched pairs test Categorical outcomes Contingency table analysis Survival analysis Diagnostic lab tests ROC curve Bland Altman plot Nonlinear regression Fitting an enzyme kinetics curve Comparing two enzyme kinetics models Automatic outlier elimination exponential decay Global nonlinear regression dose response curves Ambiguous fit dose response Explore the graph portfolio Choose the Portfolio tab at the bottom of the Welcome dialog to browse dozens of polished graphs each of which demonstrates several Prism features 1995 2014 GraphPad Software Inc 12 GraphPad Prism User Guide When you open a portfolio graph you ll see a brief explanation of how that graph was made and can explore the details Many of
446. want to create a new graph from the transposed data fi Parameters Transpose X and Y i Transpose into which kind of table xY table Grouped data table Row titles of new table Column titles of original table ABC None X values of new table jumn bile Data set column titles of new table Row titles of onginal table values of onginal table Row numbers of orginal table New graph 7 Create a new graph of the results An alternative way to transpose is to copy selected data and then paste transpose 1995 2014 GraphPad Software Inc 356 GraphPad Prism User Guide Don t confuse transposing a data table making each row become a column with swapping X and Y columns so X becomes Y and Y becomes X If you want to swap interchange X and Y columns this is possible via a checkbox on the Transform dialog 18 6 Prune rows This analysis takes a large table and creates as output a smaller table which can be easier to work with But note that your original data are still part of the file which means the project file gets larger not smaller But it can be useful to have a smaller data set for quicker analyses and graphing To prune click Analyze and choose Built in analyses Then choose Prune from the list of data manipulations to bring up this dialog s Parameters Prune Rows Options Exclude all rows where X is too low oe too high X range to keep From 1 000000e 01
447. will show as the default drawing button on the main Prism toolbar 2 Position the mouse pointer now a pencil at one end of the line or arrow or one corner of the box or oval 3 Hold down the primary mouse button and drag to the other end or to the diagonally opposite corner Hold the control key if you want to draw a perfect circle or square Changing the appearance of a drawing object line arrow square etc Select any object or several objects and double click on it to bring up the Format Object dialog Choose the thickness color and style of lines or borders the fill color and shading of shapes and arrowhead direction size and style For a line for example you can choose to have no arrowheads or arrowheads on one or both ends You can also choose to caps on the ends of a line instead or arrows 1995 2014 GraphPad Software Inc GraphPad Prism User Guide f Format Object Lines Arrows amp Arcs Border Thickness 2Qpt Thickness Colo Si Color x Stile y Style Arrowheads Interior Direction Fill x Arrowsiz Pattern Styl ar attern Color v Position Cancel You also can right click on any drawing object to change individual properties like color and line thickness 20 4 Including pictures and other objects To paste a picture or object from the clipboard Copy a picture in the other program then paste onto a Prism graph or layout
448. with normality test or perhaps create a Frequency Distribution The first line of the script specifies which data table will hold the results Then the script loops 100 times With each loop it goes to the first results page with the simulation and regenerates with new random scatter It then goes to the second results page with curve fit results and writes the value in the fifth row of the first column into the data table and labels that column logEC50 You will want to adjust the row number and perhaps add additional lines to output additional results You may also want to loop more than 100 times 17 5 How Prism generates random numbers Random or pseudo random The only way to generate truly random numbers is through a random physical process such as tossing dice or measuring intervals between radioactive decays Prism like all computer programs generates random numbers from defined calculations Since the sequence of numbers is reproducible mathematicians say that the numbers are pseudo random The difference between truly random and pseudo random numbers rarely creates a problem For most purposes computer generated random numbers are random enough to simulate data and test analytical methods Prism uses the time of day when calculating the first random number so you will get a different series of random numbers every time you run the program Random numbers from a Gaussian distribution Prism generates rando
449. wo similar graphs of different data you ll want to duplicate the family or clone the graph Clone a graph Cloning means to duplicate a graph along with data tables and results included on that graph Enter a new data set and it will instantly be graphed the same way Clone a graph when starting a new project from the Welcome dialog Or drop the New button and choose Data Table Graph 1995 2014 GraphPad Software Inc Work efficiently Repeat analyses and graphing 95 New Data Table and Graph i x 2 Opened project Y Projecti XY ky Column Grouped Contingency Survival Parts of whole Clone a graph Choose to Clone from an open project a recently used project or a Prism project that you have saved as an example or has been saved as a shared example Prism will show a dialog where you can choose which data and titles to delete By default Y values are deleted but X values and titles are kept Clone Example Example Data Subcolumn Format Preview Example data Delete Y values E Delete X values E Delete column data set titles se 2 eg nnn Delete row titles Title of the cloned table Data 1 Q amp A e Are analyses also cloned It depends Cloning duplicates regression lines and curves and results tables that are included on embedded tables Other analyses that are linked to the original data table but are not included on the grap
450. xporting data from Excel to Prism Although Prism can open Excel files this is slow Instead write a Visual Basic macro to export selected values as a text file The macro below run from Excel exports the 1995 2014 GraphPad Software Inc s GraphPad Prism User Guide upper left corner of worksheet 1 12 rows 6 columns to a comma separated value CSV file which Prism can import Open C data july97 dr2 csv For Output As 1 For I 1 To 12 For J 1 to 6 Print 1 Worksheets 1 Cells I J Value Next Write 1 Next Close 1 Follow this with code to launch Prism run the Prism script and perhaps import results from Prism back to Excel Creating a PZC Prism script file from Excel While creating a system to run Prism from Excel you need to edit both the Excel VBA statements and the Prism PZC script One way to simplify your work is to write Visual Basic code that exports the PZC file from Excel Then you only have to edit one file For example you could use the following VBA code Open C Prism4 auto pzc For Output As 1 Print 1 Shortlog Print 1 SetPath C gp prism25 Print 1 Open generate pzm Print 1 openOutput fit txt Print 1 ForEach 500 Print 1 GoTo R1 Print 1 Regenerate Print 1 GoTo R 2 Print 1 WCell 5 1 Print 1 Next Close 1 Shell C program files prism5 prism exe C prism5 auto pzc The first line st
451. y ANOVA 1995 2014 GraphPad Software Inc What s new in Prism 6 19 GroupA GroupB_ Groupe jata Set Groupa GroupB Group SetB Data Sat t id a er ata oer al A Y1 A Y2 B Y1 B Y2 C 1 C Y2 1 2 3 pm A Y1 A Y2 B 1 B Y2 C V1 C Y2 Group A Group B Group C d Data SetA Data Set B Data Set PEB a avi Aa y2 By B Y2 C 1 c v2 1 E pmm m Group A Group B 3 i Data Set A ata Seto 2 4 What s new Regression Simpler e Much easier interpolating Many people use nonlinear regression for the purpose of interpolating values from standard curves If that is your goal most of the options provided in the nonlinear regression dialog are neither required or helpful Prism 6 offers a new analysis just for interpolating curves It offers only essential options so is super easy to use e Plot functions to understand them Before using an equation as a model to fit to data it is wise to first understand it A great way to do this is to plot the function and see how it changes when you alter the parameters Prism plot functions using an analysis called Generate a family of curves It addition to or instead of plotting the function itself Prism 6 can now also plot the first and second derivative of the function and its integral Fit more kinds of models with nonlinear regression e Implicit and dif
452. y data EE idii haa Pe s eee Interleaved bars Plot Moan e More subcolumns Prism 6 allows up to 256 subcolumns for replicates Prism 5 alowed only 52 1995 2014 GraphPad Software Inc What s new in Prism 6 33 2 12 What s new Layouts e Unlinked graphs Prism 6 lets you assign a graph to a layout as an unlinked picture that won t update if the data are edited or replaced or if the graph is altered One use for this is if you want to make several versions of a graph sequentially and place each on a layout Resize graph to match length of X axis The resize graph dialog in Prism 5 lets you change the graph size to make the entire graph object have a specified width But sometimes your goal is to match the length of axes rather than the size of the entire graph object including labels Prism 6 now lets you specify the desired length of the X axis and the rest of the graph changes size to meet that goal Control the scaling factor on a layout When you place a graph on a layout its size usually changes For example the total length of a graph might be half as long on the layout as it is on the graph We now term this value 50 the scaling factor If you then add a legend drawing or image to the graph Prism 6 will maintain the scaling factor so the graph itself won t change size on the layout but the graph plus its legend drawings etc will get larger In contrast Prism 5 maintained the size of the graph
453. y end up with some data sets with one kind of error bar and other data sets with a different kind of error bar 1995 2014 GraphPad Software Inc 150 GraphPad Prism User Guide 11 3 Replicates and error bars on Column graphs Column tables offer no choices for data entry A Column table has no subcolumns Replicate values are stacked into each column Note the distinction between this arrangement of data and the arrangement used in XY and Grouped tables where replicates are placed in side by side subcolumns When creating a Column table you have no choices for data entry Learn more about Column tables If you want to create a column graph but enter error values computed elsewhere you can t do so on a Column data table Instead create a Grouped table but enter data only into the first row A Grouped graph from data entered on one row looks like a Column graph Choosing how to plot error bars and or replicates The Welcome dialog not only lets you choose the basic type of graph via thumbnails on buttons it also lets you choose how to plot replicates or error values via the drop down list The choices in the drop down list change depending on which kind of graph you choose Changing how replicates or error bars are plotted To plot the replicates or error bars differently you don t have to remake a graph Instead click the Change graph type button Change Gle Li a a P The changes you make on the Change Type of
454. ynote Send 2 9 Ov The Send to PowerPoint command copies the current graph or layout creates a new slide in PowerPoint and pastes When you send to PowerPoint it matters what the background color is in Prism If the background is CLEAR in Prism then Prism leaves the background alone in PowerPoint If the background is any color in Prism including white then Prism changes the PowerPoint background to match If your PowerPoint slide master has a background gradient or image that you want to keep make your backgrounds in Prism clear not white Send to Word Windows only Send a 6 The Send to Word command copies the current graph or layout or a set of graphs or layouts selected on the gallery and pastes it into Word Position your insertion point in Word before using this button This button is available on Prism Windows but not Prism Mac Setting preferences for Send to Word or Send to PowerPoint Windows only Open the Send to MS Office tab of the Prism Preferences dialog 1995 2014 GraphPad Software Inc 308 GraphPad Prism User Guide r Preferences View Fie amp Pines NewGraphs Analysis Internet Into Sheet File Locations Send to MS Office Send a graph or layout to Ward or PowerPoint as Embedded object recommended Linked object Only for MS Office XP or greater Picture only No link Choose EMF vs WMF format on the File amp Printer tab Wapping style in Word i Use Word s
455. you when the script is complete If you run a script fromthe script dialog every step is logged in the second tab of the dialog In this case the CreateLog command is ignored as the log is always created If you run a script from a file the CreateLog command starts logging every step into a file with the same name as the script file but the extension log SetSheetTitle renames the sheet If you specify K the first K characters of the sheet name are retained and the rest is renamed The Print command prints just the current sheet The Exit command closes all open files without saving and without prompting to save and exits Prism It works on Windows only 23 3 Running a Prism script Running Prism scripts There are several ways to run a Prism script While testing and developing a Prism script run it from Prism Once you perfect it you may want to run it fromthe command line or from another program as explained in this section 1995 2014 GraphPad Software Inc 440 GraphPad Prism User Guide 23 3 1 Creating and running a script from Prism Creating and running a Prism script within Prism While testing and developing a Prism script run it from Prism Once you perfect it you may want to run it from the command line or from another program as explained later Creating a script To create a script within Prism 1 Click the Prism button or drop file menu and choose Run Script 2 Choose to make a new script 3 C

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