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MasterPlex® - Hitachi Solutions America

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2. Current Page 1 Total Pages 17 Zoom Factor 130 Figure 6 12 Print Preview 2 To print click the Print amp icon from the menu bar Print setting dialog appears E NOTE For more printing options see appendix A section A 2 Print Preview menu MasterPlex EX www miraibio com 83 CHAPTER7 DATA CHARTS CHAPTER 7 Data Charts Charts tab MasterPlex EX can display MFI count or concentration data in many graph formats in the charts tab Charts tab ez tel roug selected analytes in swell Sample ALAL Ae fis FUPCR hE MF Selected Anahyrir Figure 7 1 Chart tab 7 1 Viewing a Data Chart 1 Click the Well Selector 3 button A mini sized well plate is displayed under the button Figure 7 2 MasterPlex EX www miraibio com 84 CHAPTER7 DATA CHARTS Unk3S Unit UnkS2 Unk Sim EGER nics Unit Unk2t Unk29 Unk37 UnistS UnkS Unkto SH SHE ue Unita Unkz2 Unka0 UriGB Unt UrkS Unk 2 0 Figure 7 2 Well Selector 2 Select the wells you want to display on the chart You can select multiple wells by pressing CTRL key Figure 7 3 Figure 7 3 Multiple Well Selection Selected analytes in well Bi MH rem Lux 00505 Lagoa m Em XXX a KM E LLLI LU zum iom a T Hor Frig 1 1 Bate 1 in 12 4 1 5 i Dna TE alpha Sakti Anahi Figure 7 4 Multiple Well Selection MasterPlex EX www mir
3. House Keeping Gene A cc A cxcuo A ran Figure 4 45 Renaming box Rename ACTE 2 Input new name and click out side of the box or enter return key Renaming is performed Figure 4 46 EA ouse Keeping Gene S oaa is A co Be CXCLS Rename GAPD apn Figure 4 46 Renaming the analyte name MasterPlex EX www miraibio com 62 CHA PTER4 DEFINING A PLATE 4 11 Quality Control Manager optional module Quality Control Manager helps you flag and optionally set as an outlier any wells whose value is outside of the range defined by the thresholds Thresholds can be assigned using the manual method for A single selected analyte Multiple selected analytes All analytes To open the Quality Control Manager Figure 4 47 click the Quality Control Manager button jy Quality Control Manager All analytes This tool helps you flag and optionally set as an outlier any well whose IE Value is outside of the range defined by the thresholds Thresholds can r be assigned using the Manual method for Analyte A single selected analyte Multiple selected analytes All analytes After each change please click the Apply button to Save Flagged wells 2 Mark as outlier nd Ce Lower Upper Response Values Calculated Values Figure 4 47 Quality Control Manager dialog The software automatically marks wells that contain data less than the user MasterPlex EX www mi
4. lt xml versionz 1 0 encoding utf 8 7 gt lt MasterPlexPlateData gt Row lt Row gt lt Cols12 lt Col gt FileName gt lt PlateName gt lt PlateT ype gt 1 lt PlateType gt zRunDate gt zRunTime gt lt AnlyDate gt lt AnlyTime gt lt Operator gt lt LXVERSION gt lt LXHWSN gt lt BeadiInfo beadname GM CSF id 0 bkgvalue 0 stdunit pg mL gt lt Beadinfo beadname IFN gamma id 1 bkgvalue 0 stdunit pg mL gt lt Beadinfo beadname Il 1 Beta id 2 bkgvalue 0 stdunit pg mL gt zBeadInfo beadname IL 10 id 3 bkgvalue 0 stdunit pg mL gt zBeadInfo beadname IL 2 id 4 bkgvaluez stdunit pg mL gt lt Beadinfo beadname IL 4 id 5 bkgvalue 0 stdunit pg mL zBeadInfo beadname IL 5 id 6 bkgvalue 0 stdunit pg mL zBeadInfo beadname IL 6 id 7 bkgvalue 0 stdunit pg mL gt lt Beadinfo beadname IL 8 id 8 bkgvalue 0 stdunit pg mL gt BeadInfo beadname TNF alpha id 9 bkgvalue 0 stdunit pg mL gt lt Well wellid L type 0 name addr A1 group 1 replicateid dilution 1 ignorewell wellcolor rowid 1L colid 1 refctriwell gt lt Bead id 0 mfi 92 conc 0 count 204 statusz 1 constr resstddey 0 sampleayg 0 samplecy 0 constddev 0 conavg 0 concv 0 normfiz resulthdrz z Bead id 1 mfi2Z 2836 conc 0 count 1490 status L constr resstddev 0 sampleayg 0 samp
5. 121 Plate Tab Toolbar ER Vs whew ee he KUNDE UN a Mad te 122 Data Table Tab Toolbar VA WAA SR RER EE GARE NM MR RR ADURE ESS 123 Chart Tab Toolbar REESE RD VA RUP RO Rb OUV ROV TOS eke XU DRE UR 125 Export Manager Tab Toolbar Prnt 126 MasterPlex EX www miraibio com ILI CHAPTER 1 WELCOME MiraiBio MasterPlex EX CHAPTER 1 Welcome to the MiraiBio MasterPlex EX User Manual MasterPlex EX software analyzes results files csv xls xd or mlx from the Luminex 100 200 or BioPlex system 1 1 About This Manual This manual explains how to use the MasterPlex EX software to Import results files csv xls Ixd or mlx from the Luminex system Designate control treatment and background wells Set housekeeping gene Normalization and compute fold change Generate data charts and reports What s New in MasterPlex EX MasterPlex EX offers new features including the ability to Merge plates using virtual plate feature so that it can analyzes beyond 100 panels at one time Make a sample marking and groups easily and quickly using Auto grouping feature or dragging grouping feature Calculate a fold change for being used relative gene analysis Normalize the data so that 1t can analyze between different plates Generate a custom reports using style sheet Conventions Used in This Manual This manual describes the steps required to perform the various tasks associated with the MasterPlex EX software The manual use
6. 2 Click the Load button The template is applied and the properties are set to the current chart Overwriting a Template You can overwrite an existing template with the current chart properties 1 In the Chart Template Manager select the template that you want to overwrite 2 Click the Overwrite button A confirmation box appears Figure 7 14 Warning x A Are you sure you want to overwrite v analvte x MFI black Figure 7 14 Confirmation box MasterPlex EX www miraibio com 95 CHAPTER7 DATA CHARTS 1 Click OK to overwrite the selected template with the current chart properties Exporting a Chart Template You can export a template to a user specified location 1 In the Chart Template Manager click the template you want to export 2 Click the Export button c The Save As dialog box appears Figure 7 15 Save in E examples v Oo jm mE 1 p x5 My Recent L ocuments 2 Desktop My Documents P My Computer 4 File name My Network Save as type MasterPlex Chart Template 7 mxtc Figure 7 15 Save As dialog box 3 Choose the directory for the template that you want to export 4 Enter a name for the template mxtc oF NOTE A template must have a mxtc file extension Changing the extension will render the exported template unusable Importing a Chart Template You can import a chart template mxtc from a user specified location MasterPlex EX www miraibio com
7. 54 00 6 0 00 C Set data type as sample amount in the Sample amount is shown in the well grid upper or lower dropdown list LJ 2 00 11340 00 11340 00 n EF 1 nan EETA ee Click one of the Click same well again Input the value Click other well well you want to press character key or enter key or input the value press F2 to enter the ESC key to exit edit mode the edit mode Figure 4 16 Input manually using edit mode MasterPlex EX www miraibio com 39 CHA PTER4 DEFINING A PLATE 4 3 Linking a Control Group Treatment wells must be associated with or inked to the control group that will be used to calculate fold changes By default the first control group that you define will be linked to the treatment well groups If there is more than one control group on the plate you can link a user selected control to a user selected well group s 1 To link a well group to a control group press and hold the Ctrl key while you click the group and the control group that you want to link NOTE A control group can be linked to multiple groups of the same well type but each group can have only one control group 5 2 Click the Link One vs Multi button l 3 To check the status select Link Group data type from upper or lower drop down Figure 4 17 ET E uu 3 54 1 Ctrl 1 Ctrl 1 Ctrl 1 Ctrl 1 Ctrl 1 Ctrl 1 Ctrl 1 Ctrl 1 cil cti ctrl 1l Ctrl 1 Ctrl 1 chil ct ctrl 10 Ctrl 1 Ct
8. 96 CHAPTER7 DATA CHARTS 1 In the Chart Template Manager click Import button The Open dialog box appears Figure 7 16 Look in 23 examples A My Recent Documents B Desktop LJ My Documents My Computer Hle name My Network Files of type MasterPlex Chart Template mxtc Figure 7 16 Open dialog box 2 Choose the directory with the template that you want to import 3 Select the template and click Open The template name is added to the Chart Template Manager Deleting a Template You can delete a template mxtc from the system 1 In the Chart Template Manager click the template that you want to delete 2 Click Delete button A confirmation box appears Figure 7 17 MasterPlex EX www miraibio com 97 CHAPTER7 DATA CHARTS Warning x AN Are you sure you want to delete y analyte x MFI black Cancel Figure 7 17 Confirmation box 3 Click OK to delete the template The template is removed from the Chart Template Manager WARNING This permanently removes the template from the system WARNING MasterPlex EX www miraibio com 98 Tf Printing a Chart You can print your data with the Print button 1 Click the Print Preview button Print preview window appears Figure 7 18 9 Preview File View Background ETYENUUTTUUEUMRNIESUVEUCUPETHEN UU Selected analybes in well
9. CE Unienawn 1 aim 540 89 202 12821 813 26 Unkina 1 11300 54188 218 35458 671 22 Figure A 13 Example of the text and image watermark MasterPlex EX www miraibio com 120 APPENDIXB MASTERPLEX EX TOOLBARS APPENDIX B The toolbars that are available depend on the types of windows that are open in the main display area B 1 Main File Menu and Toolbar Table B 1 Main File menu and toolbar Menu Bar Main Function Command Toolbar Button File Open Displays the Open dialog box so that a Luminex results file csv Ixd BioPlex file xls or MasterPlex EX file mlxe may be opened File Close Close currently opened plate data file File Save Save currently opened plate data File Save as EM Save currently opened plate data as different file name L File gt Recent Files List up the files recently opened File Exit Analyte Filter b d Valid analyte filter feature Virtual Plate x Generate virtual plate It opens plate dimension d input dialog Windows Show Close MasterPlex application a Set tab style window display Tab style Windows gt Arrange the window by cascade style Cascade Windows Tile Arrange the window by horizontal style Horizontal Windows Tile Arrange the window by vertical style MasterPlex EX www miraibio com 121 APPENDIXB MASTERPLEX EX TOOLBARS Vertical Tools Open application license information dialog Applications Tools gt Plugins Open plug
10. CHAPTER5 NORMALIZATION amp FOLD CHANGE 2 Fold changes are calculated after normalization calculation Figure 5 15 Plate Map Dashboard Data ACTE Acc Control Treatment MFI Sample Chart A cxeis 1280 00 Y 033 4 2 57 EA GAPD g EETA Correlation 0 9980 amp cami i A FNG A n6 d MAPKS d TFE amp THF i 500 1000 1500 2000 Ctrl 1 Ctl 2 Ct 3 Cul 4 C puce sample Amount Normalized by House Keeper Gene ACTB 700 1 ACTE MFI 600 s ACTB N MFI 500 E ras 300 04 amp 200 100 F3 e RENS M PPP PPPS PH EPO PE HEPA DA hp pp mpm 34 ee ee ee ee ee ee ee ee a i a a a i i PAAPA A LEE EER ERE TERETE REL ER ERE EEE PREBOOOOE POP MMEPSESOMAMEARAREREROINAD EREBREREEERERERERESRSSESRERREBR EES B Samples Well Position Figure 5 15 Fold Change Calculation MasterPlex EX www miraibio com 15 CHAPTER 6 CHAPTER6 REVIEWING DATA Reviewing Data Data tab Data tab is to review the data across all analytes In this tab you can Add or delete the data column via column selector box Sort or filter the column data Change the column layout Make groups to categorize the data Print or export the data Data tab mi Sr HTE Gram Mira Pr zl Lom J aL Sargin EL ju Ej EpnpEHT 1230 4X CI arca CI ZEB Dri 5enpepit i34 5d EL erpai ERN Fy 5pnpie Fy 43 ik al roa Gl 12 00 RL benii Hi 15 RI Damc RI LH Er omie p OI tampm C 10d D Spend D iM EI
11. EMEN chart Sekescked arabes in wel Swapit K1lALI fis Customize chart properties Print or export the chart Export Customized Data or Transform the MasterPlex QT xml data to original data format mport or export the style sheet data mpm MasterPlex EX www miraibio com 17 CHAPTER3 GETTING STARTED 3 6 Viewing Data in the Plate Tab The EX application module starts 1n the Plate Map tab If any other tab page 1s displayed click the Plate Map tab to display the Plate Map tab as shown below Figure 3 6 Plate Map tab rt E F E 3 j a u t Be woe bl 528 0 SLANI 113 ieu E Im FEE anl jo 2m 1 00 PH 213 00 LN TL an 1i Er a in 21 187 a4 121 X Rum auum o 5 xh huh m Figure 3 6 Plate tab page 1 If more than one application window is open select the Ej Cascade E Tile Horizontal or T Tile Vertical menu from the window menu bar to arrange the application windows for easier viewing 2 To change the data displayed in the well grid a Click an analyte in the Analyte pane b Make a selection from the data type upper drop down list The well grid displays the data for the selected analyte MasterPlex EX www miraibio com 18 CHAPTER3 GETTING STARTED Figure 3 7 shows the components of the Plate tab Table 3 1 lists the types of data available for display in the plate view 3 To view background subtracted data click the Subtract background b
12. Sort Descending Sort right clicked column by descending A Clear Sorting Clear sorting of right clicked column if the MasterPlex EX www miraibio com 107 APPENDIXA PREFERENCES Group By This Column Make a group by right clicked column The Hi group is located under the last position of current group hierarchy Hide Group By Box Display Hide Group Box Figure A 2 on the upper side of the columns It enables you to TTL make group s by drag and drop operation Remove This Column Remove right clicked column Column Chooser Show Column Chooser box BEEN Adjust the width of right clicked column Clear Filter Clear filter condition of right clicked column 1f column is filtered Filter Editor Open Filter Builder window Figure A 6 Best Fit all columns Adjust the width of all columns TE il J Group Box The Group Box appears on the upper side of the column Figure A 2 by choosing the Group By Box menu from the right click menu on the grid column You can drag one of the column you want to group to this box Figure A 3 Also you can multi group by repeating same way Figure A 4 Show Columns Selector Export to File 1 Print Preview Well Sample Name Group Name MFI MFI Ay El Bead Name GM CSF A1 Background 1 41 00 Bi Standard 1 10516 00 Figure A 2 Group Box MasterPlex EX www miraibio com 108 APPENDIXA PREFERENCES
13. duplication or disclosure by the Government is subject to restrictions as set forth in subparagraph c 1 11 of the rights in Technical Data and computer software clause of DFARS 52 227 7013 Hitachi Software Engineering America Ltd 601 Gateway Boulevard Suite 100 South San Francisco CA 94080 EXPORT LAW ASSURANCES You acknowledge and agree that the Software is subject to restrictions and controls imposed by the United States Export Administration Act The Act and the regulations thereunder You agree and certify that neither the Software nor any direct product thereof 1s being or will be acquired shipped transferred or reexported directly or indirectly into any country prohibited by the Act and the regulations thereunder or will be used for any purpose prohibited by the same GENERAL This agreement will be governed by the laws of the State of California except for that body of law dealing with conflicts of law Future updates of the Software will be available for purchase by licensees for a fee provided a registration card has been received by Hitachi Software Engineering America Ltd MasterPlex EX www miraibio com 1V LICENSE AGREEMENT Should you have any questions concerning this Agreement you may contact HISAL at http www miraibio com You acknowledge that you have read this Agreement understand it and agree to be bound by its terms and conditions You further agree that it is the complete and exclusi
14. 2 Right click the selected wells and select Aspirate from the pop up menu that appears Figure 4 40 c The data for the analytes in the selected wells are added to the virtual pipette and 1s ready to dispense into a virtual plate MasterPlex EX www miraibio com 55 CHA PTER4 DEFINING A PLATE oF NOTE If the background is subtracted in the source plate the virtual pipette aspirates and transfers background subtracted values If you do not want to aspirate background subtracted values make sure the background subtraction is turned off before you aspirate data into the virtual pipette Click the LJ button to turn background subtraction on or off 1 2 3 4 41 00 39 00 37 00 112 A 10515 00 10034 50 66 00 4811 B E 3104 0 E Figure 4 37 Well grid Right click selected wells to display the pop up menu 3 To clear the data from the virtual pipette right click and select Clear from the pop up menu Figure 4 40 4 e Dispense Figure 4 40 Clear Aspirated Data MasterPlex EX www miraibio com 56 CHA PTER4 DEFINING A PLATE Adding Data to a Virtual Plate After the virtual pipette aspirates data from the source plate it 1s ready to dispense the data into the virtual plate 1 Position the mouse pointer over the virtual plate 2 Click the first well to which the data will be added 3 Right click the well and select Dispense from the pop up menu that appears The data are added to the
15. A1 BH Hga D p Dens Current Page i Figure 7 18 Save As dialog box of CHA PTER7 DATA CHARTS Zoom Factor 60 2 To print click the Print icon from the menu bar Print setting dialog appears NOTE For more print options see appendix A section A 2 Print Preview menu MasterPlex EX www miraibio com 99 CHAPTER7 DATA CHARTS 7 8 Copying or Saving Chart Image The software can export the chart image to other applications The data may be copied to the system clipboard or saved in different file formats 1 Right click on the chart you want to copy or save 2 To copy the chart image in bitmap format click Copy The image is sent to the clipboard and you can paste the image data on other applications 3 To save the chart image in other formats click Export Image The File Save dialog is opened Figure 7 19 4 Input the file name and select one of the file formats from the Save as type drop down list There are five formats available bitmap png html pdf and Excel Save in E Desktop i 4 My Recent Documents My Documents 5 My Computer si T i zi L My Network Save as type v Figure 7 19 Chart Image Export dialog MasterPlex EX www miraibio com 100 CHAPTER 8 CHAPTERS EXPORT DATA Export Data Export tab This chapter explains how to export MasterPlex EX data transformed by the user Custom report is a power
16. Figure 4 45 ULOD tab Uo CV Use CV value of the group Figure 4 52 Flag the values greater than the specified CV value fail Extrapolated Values For all analytes I Set SoC threshold as greater than 10 Figure 4 52 Outlier check boxes MasterPlex EX www miraibio com 66 CHAPTER5 NORMALIZATION amp FOLD CHANGE CHAPTER 5 Normalization amp Fold Change Dashboard tab This chapter explains how to evaluate each analyte and calculate normalized MFI and fold change 5 1 Go to Dashboard Tab Click Dashboard tab then application window displays the dashboard tab page Figure 5 1 Dashboard tab j Control Treatment MFI Sample Chart i i Gores i B AE T 5 Cereri gl na ue 23 Twy RN E ls Cami a a z n4 Click nere tn select walls 0 4 0 3 4 za T Click here to Select sells Pd Analyte list Dashboard charts area Commands and pane Display Options Figure 5 1 Dashboard MasterPlex EX www miraibio com 67 CHAPTER5 NORMALIZATION amp FOLD CHANGE 5 2 Checking the Data Distributions Using Multi Charts There are three blank charts in the charts area by default and you can use these charts for checking your data Dashboard has four type of charts Figure 5 1 Drag Drop Charts x Izd Control Treatment Chart Is Well Chart S5 Analyte Comparison Sample MFI Comparison Figure 5 2 Four chart types Table 5 1 Charts Chart Name Descriptio
17. Figure 5 6 Normalized by Geometric Mean CCL MF COL N MFI ISIN Psz i Euow J 3 E 7 o x s 3 E p E T E E U VT uU L n n n LE n n n rm x Bae R288 eb XS ES BSSSRESLBI2SEBSZSE les Well Position Normalized by Geometric Mean 16 IFNG MFI A 14 IFNG N MFI UCM LA Copy Export MFI Display MFI lJA paz Eeulo v vw Display Normalized MFI vi Line Graph Area Graph zy zy dwe E E mu m A gt igh lg aie ii He T ic galzow E ap Lo p ii res La m ul ik it oO i Lad 3 8 2 Samples Well Position Figure 5 6 Context menu for Well Chart MasterPlex EX www miraibio com 70 CHAPTER5 NORMALIZATION amp FOLD CHANGE Analyte Comparison Chart Analyte comparison chart plots all MFI or normalized MFI data between two analytes with correlation line Figure 5 7 Chart can be copied or exported from context menu and display data type can be chosen from context menu as well Figure 5 4 1400 1200 1000 800 ACTE Analyte Comparison Y 0 24 x 102 0 Correlation 0 4889 300 600 900 1200 1900 1800 2100 GAPD Figure 5 7 Analyte Comparison Chart 1400 1200 1000 00 ACTB 600 40 200 Analyte Comparison Y 40 24 x 0 102 4 Correlation 0489 smi u e Copy Export w Display MFI Display Normalized MFI 0 500 100
18. argi Ir ea wed T I ES ul E3 El lick here to select well Dep Drop Certa ice Tran ruri Chari Figure 5 12 Replace the chart by drag amp drop MasterPlex EX www miraibio com 73 CHAPTER5 NORMALIZATION amp FOLD CHANGE 5 3 Normalization and Fold Change Selecting a Normalization Method 1 Select an analyte from the left analyte pane 2 In the normalization option pane select one normalization method from the drop down list Figure 5 13 Some methods needs to specify the normalization baseline item Normalization Options X Geometric Mean Figure 5 13 Model Equations drop down list Table 5 2 Normalization methods Method Description None Nothing normalization is done Geometric Mean Use geometric mean method as a normalization baseline HK Gene Choose one particular housekeeping gene as a normalization baseline HK With Least Automatically select a housekeeping gene which has least lt CV CV value as a normalization baseline Constant Use user inputted value as a normalization baseline Inter Sample Use inter sample factor method as a normalization Factor baseline Calculate normalization and fold change 1 Click Calculate button in the commands pane Figure 5 14 If you want to calculate for all analytes at the same time check All Analytes check box Commands A w All Analytes el Calculate Figure 5 14 Model Equations drop down list MasterPlex EX www miraibio com 74
19. com 21 CHA PTER4 DEFINING A PLATE Table 4 1 Sample mark icon and context menu to define wells Well Type Button Context menu on the well erid Background Background Wells that contain no analytes Control Control Wells that contain analytes that function as C controls for a particular assay design Treatment Treatment Wells that contains analytes of unknown concentration Unmark Unmark Clear the current marking A oF If a well belongs to a group unmarking the well also removes the well from the group 3 Repeat step 1 and step 2 to mark and group other well s Designating Well Groups After you have defined the wells the wells are organized into groups automatically so that the software can identify Replicate unknowns MasterPlex EX automatically places all background wells into one group You can define one or more groups of control wells per plate MasterPlex EX www miraibio com 28 CHA PTER4 DEFINING A PLATE oF NOTE A group can include nonadjacent wells A plate can have more than one group of controls or unknowns Grouping Wells by Pattern The purpose of pattern grouping is to provide users another way to easily and quickly make replicate groups Pattern here means two things the group type e g control unknown and the dimensions of the group 1 e rows and columns This function acts similarly to the Resizing feature of Microsoft Excel It is especially useful when the plate has man
20. diluted sample amoount value for each replicates use replicate filling option Figure 4 13 Figure 4 14 and 4 15 shows each Side by Side and Stacked replicate example Auto Fill Dilution Parameters Analyte Target Wells Highest Value Dilution Factor Unit Replicate Options Replicate Number Replicate Orientation Details Dilution Direction All Stdoo1 10000 0000 Choose Replicate Number from 2 to 5 Side by Side If replicate number is selected Side by Side other than None Side by Side and Stacked are selectable Stacked AAE L8 la Figure 4 13 Replicate Options MasterPlex EX www miraibio com 37 CHA PTER4 DEFINING A PLATE 10000 00 M 10000 00 39 06 39 06 m lA Replicate Number 2 977 Replicate Orientation Side by Side Dilution Direction iba 625 00 v di u 1 78 13 ak 0 31 0 31 Replicate Number 3 Replicate Orientation Stacked Dilution Direction c 0 0 0 0 3 o o oo E sls Figure 4 15 Stacked Replicate Options MasterPlex EX www miraibio com 38 CHA PTER4 DEFINING A PLATE Input Sample Amount value Manually If your sample amount series does not have sequential diluted values use direct edit mode on the well grid Figure 4 16 1 2 18 00 0 00 C A 0 00 c 1158 00 B 0 00 c C 1280 00 0 00 c k D 289 50 0 00 c N MFI Average s N MFI Stdev Fold Change Average Ere 0 00
21. for the installation HDD 512MB or higher for Windows XP Vista 7 Input devices Keyboard and mouse or other pointing device Memory RAM Video RAM 32MB or higher Monitor resolution XGA 1024x768 pixels or higher 1280 x1024 recommended 16 bit color high color or higher CD ROM drive Required for CD media version Not applicable for download version software Requirements Operating system Microsoft Windows XP Vista 7 Microsoft NET3 5 framework and Windows Media Player 10 or higher required MasterPlex EX www miraibio com CHAPTER2 INSTALLING MASTERPLEX 2 2 Installing MasterPlex 1 Insert the MasterPlex CD ROM in the workstation computer c The installation guide begins automatically and the InstallShield Wizard appears Figure 2 1 im MasterPlex InstallShield Wizard Welcome to the InstallShield Wizard for MasterPlex The Installshield R Wizard will install MasterPlex on your computer To continue click Next WARMING This program is protected by copyright law and international treaties Figure 2 1 InstallShield Wizard Welcome screen 2 To continue the installation click Next c The destination folder confirmation window appears Figure 2 2 MasterPlex EX www miraibio com 4 CHAPTER2 INSTALLING MASTERPLEX iz MasterPlex InstallShield Wizard Destination Folder Click Next to install to this folder or click Change to install to a different f der Insta
22. for well C1 dh Cheeks mica Hm ered p ood pa fe mra A Selected analytes in well C2 Fae zum rud Ceara TanTaBofime gt Ab s Ted E m Farri Latrate acd Warina Tap E HOT Hood A d xn is I IZ TH ia TE eC 10 lL z l4 L i us Seected Analyte eng Verto Armen MF fot bel i elias ey Lig viies LE I 4 Hare hye TEE i d p mii ha Enos d Figure 7 11 Multiple Well Selection MasterPlex EX www miraibio com 92 CHAPTER7 DATA CHARTS Table 7 4 Chart Properties Properties Icon Features Legends FS Customize the legend s properties Diagram Customize the diagram s properties Axes Customize X and Y axes of the diagram Note that you may select an axis to be modified on the chart preview Chart Titles Add chart titles to be displayed within a chart Point Labels Customize point label properties of the selected series Note that you may select a series to be modified on the chart preview Customize series view properties of the selected series Note that you may select a series to be modified no the chart preview Choose a palette to color series or their data points Also choose the style which specifies the chart s appearance depending on the current palette Series Views Appearance bo MasterPlex EX www miraibio com 93 CHAPTER7 DATA CHARTS 7 6 Chart Template You can save the chart properties as a temp
23. virtual plate in the same configuration as in the source plate Figure 4 41 oF NOTE If the number or names of the analytes in the virtual pipette is different from that in the virtual plate the virtual analyte filter automatically appears For more information on using the filter see Working With the Virtual Analyte Filter on section 4 9 oF NOTE Data in a virtual plate cannot be removed but can be overwritten 1 Open a mlx or csv 10515 00 10034 50 66 00 49 B inse L mn 2 Select the wells of interest in the source eese plate csv or mlx Right click the C selected wells and choose aspirate from the pop up menu ER 4 D iS 1 2 3 3 In the virtual plate select the first well where you want to dispense the data A MasterPlex EX www miraibio com 57 CHA PTER4 DEFINING A PLATE 4 Right click the well and select 1 3 EL Dispense from the pop up menu Ps Clear 1 xal 1 2 3 5 The data are added to the virtual plate starting at the selected well in the same configuration as in the source plate 10516 00 5152 00 3104 00 1040 00 Figure 4 41 Adding data to a virtual plate Open a source plate mlx or csv xls or Ixd and create a virtual plate click the 2 button to generate the blank virtual plate MasterPlex EX www miraibio com 58 CHA PTER4 DEFINING A PLATE 4 9 Working With the Virtual Analyte Filter In a multiplex assay all of the plate wells must cont
24. 0 1500 2000 GAPD Figure 5 8 Context menu for Analyte Comparison Chart MasterPlex EX www miraibio com 71 CHAPTER5 NORMALIZATION amp FOLD CHANGE Sample MFI Comparison Chart Sample MFI comparison chart plots MFI and normalized MFI data selected by the mini plate selection tool Figure 5 9 Chart can be copied or exported from context menu and MFI and normalized MFI data can be tuned off from context menu as well Figure 5 10 MFI Sample Chart Y D 04 yx 0 67 Correlation 0 9984 900 1200 sample Amount Figure 5 9 Sample MFI Comparison Chart MFI Sample Chart Y 0033X 2 57 Correlation 1 9980 700 600 Se 500 s Copy 400 Export 200 v Display MFI 200 Display Normalized MFI 100 500 1000 1500 2000 sample Amount Figure 5 10 Context menu for Sample MFI Comparison Chart MasterPlex EX www miraibio com T2 CHAPTER5 NORMALIZATION amp FOLD CHANGE Replacing the chart by drag amp drop Charts in the chart area can be easily replaced by drag amp drop operation 1 Select one of the chart you want to use from the drag drop charts pane Figure 5 11 Drag Drop Charts fa Control Treatment Chart EXE Well Chart 5 Analyte Comparison 5 Sample MFI Comparison Figure 5 11 Replace the chart by drag amp drop 2 Drag amp drop selected chart into the chart area you want to replace Figure 5 12 The chart is replaced Serr ee w AB
25. 1 Double click the MasterPlex icon amp on the workstation desktop The License Information dialog box appears Figure 2 5 License Information Product Mame MasterPlex EX 2010 version 2 0 0 Build 1 Machine ID of this PC f Stand alone License Mode User Name Institute Division Date ssued Licensed Version Expiration D ate Licensed Machine ID Obtain Demo License Install License File Obtain Product License Please send an email with the saved License Request File attached to the following email address register miraibio com Network Client License Mode Requires MasterPles network license server License Server IP Address l License Server Portt Server Mame License Expires f Figure 2 5 License Information dialog box 2 To view instructions on how to obtain a license lic click Obtain Product Licenses 3 After you have obtained a license click Install New License The Open dialog box appears 4 Use the Open dialog box to locate the license lic and double click the file The license is installed MasterPlex EX www miraibio com 10 CHAPTER3 GETTING STARTED 7 8 Getting Started This chapter provides a brief overview of data analysis using MasterPlex EX It also explains how to start the software import a Luminex 100 200 or BioPlex results file csv xls or lxd and the user interface components 3 1 Overview of MasterPlex EX Analysi
26. 23 There are two preference tabs Application Application specific preferences Preferences in this tab are applied to all files being opened on the EX module Plate Plate specific preferences Preferences in this tab are applied to current being opened file E s pea E E i rami ENS Figure 4 31 Preferences dialog box Application preferences Split Cell Color Color lower grid by specified color Figure 4 32 i 2 3 4 41 00 39 00 37 00 112 00 A seme eee eee eee eee eee eee 189 194 193 225 10516 00 10034 50 565 00 4911 00 208 199 203 5152 00 5299 00 39 00 5011 00 246 247 Figure 4 32 Colored lower well grid MasterPlex EX www miraibio com 50 CHA PTER4 DEFINING A PLATE Intensity Color One Color Use Bead Count value for threshold conditions Two Color Use Error Range for threshold conditions ty Col 1 2 3 4 5 6 7 8 9 10 i 10 00 9 00 19 00 6903 00 48 50 1162 00 5573 00 2145 00 443 00 187 00 E One color GSS LimeGreen m 9929 00 8989 50 6994 00 4487 00 64 00 179 00 4746 00 1005 00 209 50 95 00 8 5850 50 5807 00 1297 00 4276 00 37 50 18 00 3271 00 7722 50 104 00 45 00 C Two colors Jpper EN 2656 00 3049 00 63 50 3277 00 1846 00 109 00 1957 00 6467 00 43 00 32 00 D 1104 50 914 00 57 50 1501 00 1842 00 138 00 7233 00 5535 50 27 50 185 00 E 300 00 404 00 1396 00 433 00 133 50 15 00 6247 50 3727 50 15 00 99 00 Cli
27. 4 A2 Background i 33 00 am 194 5450 847 82 Standard i ina 2870 38 152 9509 57 284314 a Standard 1 250 00 297035 245 5 42 17 weal n Standard 1 2990 50 270 39 252 2481 25 EE g Fanii 1 1094 00 2970 39 zn 124538 282314 2 Standard 1 300 00 297035 217 50827 292314 G2 Standard 1 10400 297039 258 33575 282314 H2 Standard 1 55 00 287038 2m 18804 2843 14 a3 Unknown 1 3700 540 89 183 46450 8122 83 Unknown 1 86 00 540 88 188 24047 813 Cc Unienawn 1 3900 540 89 27 64 60 812 28 Unina 1 A100 52588 183 103 34 8712 z Unknown 1 45 00 588 am 1247 87122 F Unkina 1 3900 540 89 213 64 60 am G3 Unknown 1 45 00 520 85 207 143407 87122 H3 Unina 1 5100 540 88 i7 180 04 87132 AA Unknown 1 11200 54085 225 35275 8122 z4 Lkn 1 4501 00 540 85 zm 3855 87 81m Ca Unina 1 501100 540 89 m 3044 48 87122 D4 Unknown i 5591 00 540 89 282 4418 11 67122 E4 Unknown 1 3070 00 520 88 185 254435 POE Fa Unkmewn 1 112880 540 89 238 17748 E GA Unkmeawn 1 3 50 540 89 im 34185 EM 44 Unina 1 5578 00 52288 241 44715 sim AS Unina 1 82 00 540 89 24 31071 gx a5 Unknown 1 10550 540 89 200 34185 8122 cs Urn 1 65 00 540 89 i72 23715 mm 25 Uninen i 3883 5 52288 m 317784 gm zm uiian 1 1808 00 540 89 218 172284 8712 F5 ql 119 00 540 89 179 36503 571 22 G5 Unin 1 11100 540 89 Hi 35080 812 5 EE 53 00 540 89 am 21554 8712 AB Unknown 1 2426 5 540 89 218 212204 87122 B6 Unknown 1 18500 540 89 219 41188 82122
28. 4 00 2861 00 280 00 1484 00 1451 00 2190 00 Figure 4 34 Well grid Outlier Options Show threshold Marker MFI Count Normalized MFI Fold Change Error Range Automatic outliers 4 1022 00 5457 00 5459 00 4589 50 575 00 CHA PTER4 DEFINING A PLATE 6 7 8 9 10 126 00 1932 50 1964 00 787 00 271 00 105 06 133 50 621 50 1465 00 472 50 128 00 e 201 00 866 50 5011 50 ow 481 00 ow 511 00 3186 00 ow 2722 00 415 00 4701 00 2289 50 154 0 218 50 72 00 49 00 3372 00 1472 00 30 00 89 0 157 50 63 001 4727 00 2160 50 831 00 310 50 59 0 Show red rectangle indicator inside the grid if the threshold conditions meet the criteria Use MFI value for threshold conditions Use Bead Count value for threshold conditions Use Normalized MFI value for threshold conditions Use Fold change value for threshold conditions Use Error Range for threshold conditions Automatically check on off the outlier check box for the wells To check on click Set button To check off click Clear button MasterPlex EX www miraibio com 53 CHA PTER4 DEFINING A PLATE 4 8 Creating a Virtual Plate 1 Open the Luminex results files csv xls or Ixd or MasterPlex EX files mlx that are the data sources for the virtual plate 2 Click the Virtual Plate button 4 The Virtual Plate dialog appears Figure 4 35 Virtual Plate Plate Dimensions To create a virtual plate please enter th
29. 5 00 3070 00 180i 2 00 300 00 39 00 1129 00 11 2 00 300 00 39 00 1129 00 11 Figure 4 9 Mouse pointer changes to hand icon 2 Click the border while mouse pointer is hand icon Entire wells within the group are selected Figure 4 10 4911 00 5011 00 2990 50 5591 00 m 3070 00 180 i 10034 50 6299 00 HO 00 300 00 39 00 Figure 4 10 Selected wells MasterPlex EX www miraibio com 33 CHA PTER4 DEFINING A PLATE 4 2 Setting Sample Amount If you want to use sample amount index to confirm your MFI values are correctly gathered use the auto fill feature to help you automatically enter the sample amount 1 Click the Auto Fill button located above the well grid The Auto Fill dialog box appears Figure 4 11 Auto Fill Dilution Parameters Analyte Target Wells Highest Value Dilution Factor Unit Stdoo1 15000 0060 2 000 pg mL Replicate Options Replicate Number Mone Replicate Orientation Details Dilution Direction 1 11 L1 we EENE Figure 4 11 Auto Fill dialog box MasterPlex EX www miraibio com 34 CHA PTER4 DEFINING A PLATE 2 Make a selection from the Analyte drop down list 3 Enter the starting value for the sample amount 4 Enter the dilution factor 5 Make a selection from the sample amount unit drop down list or input the unit from the keyboard 6 To select a dil
30. 50 19 00 17 50 27 00 H SEN M RR NEN ONEOR SOCII a on a a ae eR RR aoe CR Reo a te heme oe LX 68 69 80 42 Figure 4 6 Well groups MasterPlex EX www miraibio com 30 CHA PTER4 DEFINING A PLATE 4 Once you are satisfied with the selection just release the mouse button The software will automatically finish the grouping Figure 4 7 367 00 506 50 341 00 Figure 4 7 Well groups NOTE When starting drag you can move the pointer you can move it either downwards or rightwards which results in different ways to select wells To switch between the two modes just drag the pointer back into the pattern group and then drag it out in either direction So it is determined by your first move direction when you are dragging the pointer out of the pattern group MasterPlex EX www miraibio com 3l CHA PTER4 DEFINING A PLATE 367 00 341 00 a0 4 37 00 Figure 4 8 Well groups Dragging downwards as the first move above vs dragging rightwards as the first move below MasterPlex EX www miraibio com 32 CHA PTER4 DEFINING A PLATE Select all wells within the group at one time 1 While hovering over a replicate group border the mouse pointer changes to a hand icon Figure 4 9 6 00 B 10034 50 4911 00 10 6 00 B 10034 50 4911 00 10 2 00 09 5011 00 g 2 00 6299 00 39 00 5011 00 6 4 00 2990 50 41 00 5591 00 398 4 00 2990 50 41 00 5591 00 398 0 00 1094 00 45 00 3070 00 180i 0 00 1094 00 4
31. E USE OR INABILITY OF SUCH DAMAGES OR FOR ANY CLAIM BY ANY OTHER PARTY SOME STATES DO NOT ALLOW THE LIMITATION OR EXCLUSION OR LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES TO THE ABOVE LIMITATION OR EXCLUSION MAY NOT APPLY TO YOU GOVERNMENT LICENSEE If you are acquiring the Software on behalf of any unit or agency of the United States Government the following provisions apply The Government acknowledges HISAL s representation that the Software and its documentation were developed at private expense and no part of them is in the public domain Wn MasterPlex EX www miraibio com 111 LICENSE AGREEMENT The Government acknowledges HISAL s representation that the Software is Restricted Computer Software as that term 1s defined in Clause 52 227 19 of the Federal Acquisition Regulations FAR and is commercial Computer Software as that term is defined in Subpart 227 401 of the Department of Defense Federal Acquisition Regulations supplement DFARS The Government agrees that If the Software is supplied to the Department of Defense DOD the Software is classified as Commercial Computer Software and the Government is acquiring only restricted rights in the Software and its documentation will be as defined in Clause 52 227 19 c 2 of the FAR If the Software is supplied to any unit or agency of the United States Government other than DOD the Governments rights in Software and its documentation RESTRICTED RIGHTS LEGEND Use
32. ETTING STARTED 3 4 Saving Plate Data After you import a Luminex results file csv xls or Ixd the data can be saved to a MasterPlex EX file format mlxe The mlxq file includes all data associated with a plate such as well definitions and computed interpolated or extrapolated concentrations To save results data csv xls or Ixd to a MasterPlex file mlxq 1 Click the Save button l Alternatively select File gt Save from the main menu c The Save As dialog box appears Figure 3 9 Save in 23 SampleData gt E My Recent Documents Desktop My Documents 3s My Computer File name _ My Network Save as type EX v4 0 files mike Figure 3 9 Save As dialog box 2 Confirm the default directory where the file will be saved or choose another directory 3 Enter a file name and click Save Opening a MasterPlex File mlxe 1 Click the Open button EF Alternatively select File gt Open from the main menu The Open dialog box appears Figure 3 10 MasterPlex EX www miraibio com 29 CHAPTER3 GETTING STARTED Lookin O DE IL5 Project mlx Bs AverageStd csv BHH 10Plex csv E IL5 csv Files of type All Files mix bed xls csv Figure 3 10 Open dialog box 2 Confirm the default directory or choose another directory 3 Select a file name mlxq and click Open c An application module window opens and displays the result
33. File View Background 88 Eg Hd Le Ed P 7 8 R 130 7 Rei PERPE Ug A Sample Name Group Name MFI MFT Average Count Co Bead Name GM CSF A1 Background 1 41 00 0 00 B1 Standard 1 10516 00 2970 59 ci Standard i 6152 00 2970 39 Preview Di Standard 1 3104 00 2970 39 Area Ei Standard 1 1040 00 2970 39 Fi Standard 1 292 00 2970 39 Standard 1 108 50 2970 39 Standard 1 55 00 2970 39 Background 1 39 00 0 00 Standard 1 10034 50 2970 39 Current Page 1 Total Pages 17 Zoom Factor 150 Preview Status Bar Figure A 10 Print Preview Window Table A 4 Preview Toolbar buttons and functions Icon Command Function Search specific word or value from the 2 preview document HT Customize the printing items uu JM Open preview document files prnx Master Plex EX www miraibio com 114 APPENDIXA PREFERENCES Save Save preview document by prnx format Open print dialog Print the preview document Print Setup Open print setup dialog Header and Footer Set up header and footer options Figure A 10 Set page scale KH HE s Es EZ B Hand Tool User hand icon AU AA User magnifier el m Zoom out the preview document 709 Set zoom size from the drop down list e Zoom in the preview document 4 First Page Show first page 4 Previous Page Show previous page b gt Next Page Show next page
34. For Research Use Only Part no P 33340 10202 USER MANUAL For Microsoft Windows MasterPlex EX Expression Analysis Module HITACHI Inspire the Nexl M raiBio Group 601 Gateway Blvd Suite 100 South San Francisco CA 94080 TELEPHONE 1 888 615 9600 toll free 1 650 615 7600 FACSIMILE 1 650 615 7639 TRADEMARKS Microsoft is a registered trademark of Microsoft Corporation COPYRIGHT 2009 2010 Hitachi Software Engineering America Ltd All Rights Reserved Ver P012010 20 MasterPlex EX www miraibio com LICENSE AGREEMENT LICENSE AGREEMENT BEFORE OPENING THIS PACKAGE YOU SHOULD CAREFULLY READ THE FOLLOWING TERMS AND CONDITIONS BY OPENING THIS PACKAGE YOU AGREE TO BECOME BOUND BY THE TERMS AND CONDITIONS OF THIS AGREEMENT WHICH INCLUDES THE SOFTWARE LICENSE AND LIMITED WARRANTY IF YOU DO NOT AGREE WITH THESE TERMS AND CONDITIONS YOU SHOULD PROMPTLY RETURN THE PACKAGE UNOPENED TO HITACHI SOFTWARE ENGINEERING AMERICA LTD HISAL or HISAL Distributor AND YOUR MONEY WILL BE REFUNDED The enclosed software 1s licensed not sold to you for use only upon the terms of this Agreement and HISAL reserves any rights not expressly granted to you You are responsible for the selection of the Software to achieve your intended results and for the installation use and results obtained from the Software You own the media on which the Software 1s originally or subsequently recorded or fixed but HISAL reta
35. H Last Page Show last page Multiple Pages Select multi pages to preview Color Open color picker and set the document E PE background color Master Plex EX www miraibio com 115 APPENDIXA PREFERENCES Open water mark setting dialog Figure A 10 Export the document by selected format PDF HTML MHT RTF Excel CSV Text Image Export the document by selected format and send it via e mail PDF MHT RTF Excel CSV Text Image Close preview window Insert Header Footer To insert header footer into your printing document open Header and Footer dialog Figure A 11 Select header or footer radio button then input text or items from the header footer toolbar Table A 5 in the left center or right text box Header Footer toolbar Header and Footer an nn bud a me Qari m 7 D 2 Oa jolly Font Microsoft Sans Serif 8 25pt Left center and right Header text box OK Cancel Figure A 11 Header and Footer dialog MasterPlex EX www miraibio com 116 APPENDIXA PREFERENCES Table A 5 Header and Footer Toolbar buttons and functions Icon Command Function Page Number Insert page number Page of Pages Insert current page of total pages type page number Date Printed Insert date printed Time Printed Insert time printed ya 9 i EE Insert user name who login the windows Insert the image ui Align to Top Align all headers footers to the top lev
36. LING MASTERPLEX 5 To continue click Next The Ready to Install the Program window appears Figure 2 5 iz MasterPlex InstallShield Wizard Ready to Install the Program The wizard is ready to begin installation Click Install to begin the installation If you want to review or change any of your installation settings click Back Click Cancel to exit the wizard Figure 2 5 Ready to Install the Program window 6 Click Install The Start Copying Files window appears Figure 2 6 MasterPlex EX www miraibio com 7 CHAPTER2 INSTALLING MASTERPLEX i MasterPlex InstallShield Wizard Installing MasterPlex The program features you selected are being installed Please wait while the InstallShield Wizard installs MasterPlex This may take several minutes status Figure 2 6 InstallShield Wizard Start Copying Files window 7 After the installation 1s completed the InstallShield Wizard Complete window appears Figure 2 7 MasterPlex EX www miraibio com 8 CHAPTER2 INSTALLING MASTERPLEX i MasterPlex InstallShield Wizard InstallShield Wizard Completed The InstallShield Wizard has successfully installed MasterPlex Click Finish to exit the wizard Figure 2 7 InstallShield Wizard Complete window 5 Click Finish to finish the installation and close the window MasterPlex EX www miraibio com 9 CHAPTER2 INSTALLING MASTERPLEX 2 3 Installing a License
37. Other i vw Figure 8 7 Transformed Data HTML format 3 Save to file or print from the menu button MasterPlex EX www miraibio com 106 APPENDIXA PREFERENCES APPENDIX A This appendix explains more details about Data Grid for Standard curve tab and Data Table tab and Print Preview A 1 Grid Customize Menu Grid customize menu allows you to customize your grid data viewing more flexibly and efficiently Grid Customize Menu 1s invoked by right clicking on the both grid column standard curve data grid and data table grid Figure A 1 o ee Well Sample Name Group Nat ee 5 Sort Ascending E Sort Ascending a Analyt E amp Sort Descending 9 Bead Nar Z Sort Descending i an PF i778 PUPA Ma Hide Group By Box Hide Group By Box PT i 2 Group By This Column a ci Group By This Column i Remove This Column ul Remove This Column Column Chooser i 4 Column Chooser E Best Fit teal Best Fit sss EE E TTE Bruch Best Fit Call columns l ii i Best Fit Call columns F Filter Editor Figure A 1 Grid M 32 PP Filter Editor enu in the Standard Curve tab and Data Table tab Table A 1 Main toolbar buttons and functions Icon Command Function A Sort Ascending Sort right clicked column by ascending Fl 7
38. Ps pe 35 ED Marcel Pcre Comma Sep IIL 521 0M ki Lj dss ALS WEN Mice EE cred oma sper AEn 16 Py LJ donrrenkstiorz PET a2 08 PAN Pis Ty Lon 7 39 ani LI en emper Fi 14 ATL Hap Y uia BD tal hind Ema iens End Uus H oL bie z BS hiem Explorer H 2 Fina B L Lmmy s La Parma E Figure 3 4 MasterPlex EX and Windows Explorer application windows Use a drag and drop operation to open a csv xls Ixd or mlx file s in the MasterPlex application menu bar area MasterPlex EX www miraibio com 15 3 9 Tab categorized work flow CHAPTER3 GETTING STARTED EX application module consists of five tab pages Plate Map Dashboard Data Charts and Export Figure 3 5 designed to match the work flow in a typical multiplex data analysis session Define a Plate Mark sample as Background Treatment or Control Fill out sample amount Define Housekeeping genes J JE E FREPPFRE s z d rg mwmnmHMI i m OL A 3 eh m L hi e j u P bon EAEHO Ow i i i a 5 a A Plot data on the chats and review the data distributions Normalization Calculate fold change J T i me DOC PLE o ImOEDTOR GUION DUM CES ONG ERE EDU RES ROS e E e a OM UMOR 6 MasterPlex EX www miraibio com 16 CHAPTER3 GETTING STARTED ae uw A Review all data Print or export the data Review Data by Chart Review all data on the EM a4 34 c
39. Sere 22 443 00 rl ener 4k Ga acc d H H Hg ompi HE 112 5 EJ tamm 43 114Kl E3 prog 35 CI arp cl TAM Py Enzrasha PT rii Figure 6 1 Data Tab E Eacbproarm iv nn Haren S bbe D 6 D DD b Cm on ia iM noo D DG b 06 E DG 6 06 D on bite D DEG 6 00 D p b 6 p oti Fran Hh TG ars Prec Chang Paes Cham re Ermi Lae an T D cci Dm 1 bo be qi p DG D re an bo bb dk pon D ro 10 6 00 0 05 J p pc 0 om 030 6 06 0 0b 0 3 D DG D ot 1H b 06 b 06 ax E DG Drm 0401 0 06 p 0b 24x D on p pe d bo bob gx D DEG D nuc 6 06 b gx D p Dm 043 b 06 06 qx p oC D re n et Fra Fi Pat MasterPlex EX www miraibio com 16 CHA PTER6 REVIEWING DATA 6 1 Add or Delete a column 1 Click Show Columns Selector h CslumnsSelector button Column selector appears Figure 6 2 Customization Count Fold Change Stdev MFI CV MFI Average MFI Stdev N MFI Stdev Qutlier Figure 6 2 Column Selector box 2 To add a data column select one of the data types and drag amp drop it onto the data grid Figure 6 3 me MFI MFI Background Normalized MFI N MFI As MFIAverage s 1168 00 1168 00 0 00 1280 00 zB 00 D 0n 282 50 Customization 294 50 Count 64 00 Fold Change Stdev 68 00 MFI oy 15 00 MFI Average 15 00 MFI Stdev zm N MFI 5tdev 4 00 l Outlier 2 00 2 00 MasterPlex EX www miraibio com TT CHAPTER6 REVIEWING DATA Figure 6 3 Add data type to the dat
40. T OR DISTRIBUTE TERM This Agreement is effective until terminated You may terminate it at any time by destroying the Software together with all copies in any form This Agreement will immediately and automatically terminate without notice if you fail to comply with any term or condition of this Agreement You agree upon termination to promptly destroy the Software together with all copies in any form LIMITED WARRANTY HISAL warrants for the period of ninety 90 days from the date of delivery of the Software to you as evidenced by a copy of your receipt that 1 The Software unless modified by you will perform the function described in the documentation provided by HISAL Your sole remedy under the warranty is that HISAL will undertake to correct within a reasonable period of time any marked Software Error failure of the Software to perform the functions described in the documentation HISAL does not warrant that the Software will meet your requirements that operation of the Software will be uninterrupted or error free or that all Software Errors will be corrected 2 The media on which the Software is furnished will be free from defects in materials and workmanship under normal use HISAL will at its option replace or refund the purchase price of the media at no charge to you provided you return the faulty media with proof of purchase to HISAL HISAL will not have any responsibility to replace or refund the purchase price of t
41. TA Average Fold Change Stdev Shows the Fold Change standard deviation within the group Group Link Control group associated with this well 6 2 Sort or Filter the Column Data To sort by specific column click the column title Ascending and descending are changed alternatively Figure 6 5 Descending sort Ascending sort 10476 00 9994 50 6259 00 6112 00 5551 00 3338 00 4971 00 38 00 4871 00 Figure 6 5 Sort Column Data To clear the sort right click on the column you want to clear the sort select Clear Sorting from the menu Figure 6 6 I Sort Ascending l Sort Descending Clear Sorting a Group By This Column fmm ae Ds Des Figure 6 6 Clear Sorting MasterPlex EX www miraibio com 19 CHAPTER6 REVIEWING DATA To filter by specific data in the column click upper right side of the column you want to use it as filter base Figure 6 7 Well 7 Sample Name Well C Sample Name ere oe gt Bead Name GM CSF El Bead Name GM CSF A1 A10 B1 Ci Bead Name IFN gamma A10 EJ Bead Name Il 1 Beta A10 Figure 6 7 Filter by the data in the column NOTE There is a way to construct more complex filter conditions using Filter Builder See appendix A section A 1 Create Complex Filter Criteria paragraph MasterPlex EX www miraibio com 80 CHAPTER6 REVIEWING DATA 6 3 Exporting a Data w You can export your data table data from Export to File button 1 C
42. TA CHARTS 7 4 Changing the Color Palette There are 30 color palettes available from Color Palette button o Figure 7 9 shows the palette names and their corresponding color patterns Apex aie EI Nature Colors TREALL Aspect INNEN Northern Lights HERRERO Black and White MIEIBSBSINIL 3 Office NI Chameleon Opulent EnA DT Civic B NI 1 Oriel EE NI Concourse HH EEE Origin ET NN Equity E E Paper OOOO Flow BE E 1 1 Pastel Kit EN T NETTE Foundry BL 1 1L 1E 3E Solstice EN NIMNN Grayscale mie Technic aes le In A Fog ESTEE ETE ES NE Terracatta Pie ERED Median IEEE TESI The Trees ENSZNSBEN FU Metro EIN E Trek LIBI JEN Mixed i HN Urban T Module ee Verve EEEEE Figure 7 9 Color Palettes MasterPlex EX www miraibio com 91 CHAPTER7 DATA CHARTS 4 9 Changing Chart Properties The Chart tab has great flexibility in customizing the chart To enter the chart properties dialog click Chart Properties button Zz You can choose to change the entire chart s properties or just one of them To change the entire chart s properties click body of the f button To change one of the chart s properties click small drop down arrow right side of the button Figure 7 10 Figure 7 11 shows Chart Properties dialog and Table 7 4 explains the property categories Click small down arrow mark to show the each chart s property selection Chart for well A1 Chart for well B1 Chart
43. a grid 3 To delete the column from the data grid select desired column and drag amp drop it away from the column Figure 6 4 ne MFI MFI Background Y Normalized MFI N 1168 00 1168 00 0 00 1280 00 1280 00 0 00 289 50 MFI Bam 0 00 284 50 284 50 0 00 64 00 64 00 0 00 Figure 6 4 Delete data type from the data grid Table 6 1 Data Types in the Data Table Data Type Well Bead Name Sample Name Group Name Outlier MFI Median Fluorescence Intensity Normalized MFI Fold Change MFI Background MFI Average MFI Stdev MFI CV Count N MFI Average N MFI Stdev Fold Change Description Well name Bead name User specified name for the well The group number of the well Wells that belong to the same group have the same group number Outlier status The median fluorescence intensity measured by the Luminex 100 200 or BioPlex system for a bead set count Shows calculated Normalized MFI value Shows calculated Fold Change value Background subtracted value from MFI Shows the MFI average within the group Shows the MFI standard deviation within the group Shows the MFI CV within the group The number of beads per bead set detected by the Luminex 100 200 or BioPlex system Shows the Normalized MFI average within the group Shows the Normalized MFI standard deviation within the group Shows the Fold Change average within the group MasterPlex EX www miraibio com 78 CHA PTER6 REVIEWING DA
44. aibio com 85 CHAPTER7 DATA CHARTS 3 To display another data type for the selected wells click the Data Type drop down list and select one of the data type Table 7 1 Data Types Data Type Displays MFI MFI Median Fluorescence Intensity Count Bead count Normalized MFI Calculated Normalized MFI Fold Change Calculated Fold Change 4 To change the data type click the Chart Type drop down list and select one of two chart types Table 7 2 Chart Types Chart Type Displays Well Group Analyte data for each user selected well Single Analyte Single analyte across all user selected wells Group by Analyte Wells grouped by same analyte name Group by Sample name Wells grouped by same sample name Replicate View Plotting group values is available by clicking the Replicate View button il Replicate View 1s available only on Bar style charts If you are on another type of chart when you click the Replicate View button 1t automatically re selects the Bar chart and displays the data with error bars Figure 7 5 shows an example of the replicate view chart MasterPlex EX www miraibio com 86 CHAPTER7 DATA CHARTS Selected analytes in group Standard 1 Average B ccs Stdev 3 IFM gamma E ii i Beta Average Bp Stdev E i B B 1L 6 5 1 8 Average E TNF alpha value 12201 75 1z293 75 10275 25 3459 25 GM CSF IFM gamma Il 1 Beta IL 10 IL 2 IL 4 IL 5 IL 6 I 8 TNF alpha Selected Analytes Figure 7 5 Repl
45. ain The same types of analytes bead sets with the same nomenclature The same number of analytes This is true for virtual plates as well When you add data to a virtual plate MasterPlex EX compares the name and number of the analytes in the virtual pipette to those in the virtual plate The virtual pipette will not dispense if there are discrepancies between the number or names of analytes in the pipette and the virtual plate If the number of analytes in the pipette 1s greater than that of the destination plate the virtual analyte filter automatically appears Figure 4 42 The virtual analyte filter displays a list of the analytes that are present 1n the virtual pipette It enables you to choose the analytes that you want to add to the virtual plate and 1f necessary rename them to be consistent with the number and name of analytes in the virtual plate If you add data to a virtual plate from source wells that contain different analyte names or a different number of analytes data holes are created As a result a well in the virtual plate appears blank if the analyte selected in the analyte panel is not present in the well If a plate file csv xls Ixd mlx or virtual contains data holes the concentrations cannot be calculated NOTE In order to prevent data holes if the number of analytes in the virtual pipette is less than the number of analytes in the destination plate the data cannot be added to the virtual plate MasterP
46. amma Click here to assign List of analytes Il 1Beta Click here to assian in the virtual IL 10 Click here to assign Ppsnes IL 2 Click here to assign IL 4 Click here to assign Mane Place a check IL 8 EN Click to display a mark next to an TNF alpha pus c ated drop down list of analyte to add 054 Mouse IL 2 ud tae it to the virtual 073 Mouse IFM gamma the virtual plate plate 077 Mouse IL 4 Select a name from the list to rename the analyte from the source plate Check all analytes Add all as new OK l Cancel Figure 4 43 Virtual analyte filter 3 To save the renaming assignments for use again with the same source plate csv xls or Ixd or mlx during the current session choose the Save this assignment option If you want to aspirate other data from the same source plate choose the Use last saved assignments option in the virtual analyte filter to automatically rename all of the analytes in the filter 4 Click OK gt The data are added to the virtual plate and the virtual analyte filter closes MasterPlex EX www miraibio com 61 CHA PTER4 DEFINING A PLATE 4 10 Changing the Analyte Name You can change the analyte names on plate map tab s analyte pane Figure 4 44 MFI z Count A CCL d CxXCLS EE d GAPD di cami es a FNG SU d 16 IF NI Ah TGFBI EM 7 Ah TNF Figure 4 44 Analyte pane 1 Right click on the analyte name you want to rename Renaming box appears Figure 4 45
47. ck one color and select desired color for F decreases directl with the value 42 50 40 00 7817 00 3178 00 54 50 7301 00 3625 50 1662 50 343 00 31 00 y Eo Ee A 10 00 9 00 19 00 6903 00 48 50 1162 00 5573 00 2145 00 443 00 187 00 F On netiregen T 9929 00 8989 50 6994 00 4487 00 64 00 179 00 4746 00 1005 00 209 50 95 00 One color EH c 5850 50 5807 00 1297 00 4276 00 37 50 18 00 3271 00 7722 50 10400 45 00 s e Fw colors Upper L 255 0 0 3 2656 00 3049 00 63 50 3277 00 1846 00 109 00 1957 00 6467 00 43 00 32 00 ENTE D l 04 50 914 00 57 50 1501 00 1842 00 138 00 7233 00 553550 27 50 85 00 Lower EE 0 0 192 T E main Mka 300 00 404 00 1396 00 433 00 133 50 15 00 6247 50 3727 50 15 00 99 00 F Click t lors and select desired color for th IC WO Colors and Selec esifed Color tor e 143 50 116 00 7453 00 61 00 58 00 7190 00 4878 00 2840 50 779 00 70 00 maximum and minimum value The color shifts 42 50 40 00 7817 00 3178 00 54 50 7301 00 3625 50 1662 50 343 00 31 00 H upper to lower directly with the value Figure 4 33 Example of Intensity color Plate Preferences Plate Information Original File Name Displays the name assigned to the result file in the Luminex 100 200 or BioPlex software To edit the plate name enter a new name Analyst Name Displays the analyst name entered in the L
48. ct adjacent wells press and hold the Shift key while you click the first and last well in the selection Alternatively press and hold the mouse button while you drag the mouse over the wells of interest 1 z 3 4 20 00 367 00 506 50 341 00 A ee es 53 67 765 B 1308 00 422 00 480 50 392 00 95 66 78 9 1084 50 82 00 88 00 78 00 T2 Fo 75 7 525 00 88 50 82 00 96 50 D T 2 2 2 2 rg 66 Jb T4 201 00 37 50 38 00 37 00 81 82 85 96 66 50 32 00 32 00 34 00 F ee ee ad r9 66 74 38 00 18 00 18 00 23 00 3 wee eee ee Figure 4 2 Well grid To select nonadjacent wells press and hold the Ctrl key while you click the wells of interest MasterPlex EX www miraibio com 26 CHA PTER4 DEFINING A PLATE Designating Well Type Table 4 1 shows the types of wells that are available 1 Select the well s that you want to define 2 To define or mark the well s click one of the icons located on the upper well grid Figure 4 3 You can also right click the selection and choose a well type from the pop up menu that appears Figure 4 4 Table 4 1 c The well type is applied to the selected well s ious Figure 4 3 Sample mark icons 1 3 4 10 00 9 00 16 00 17 00 k A Aspirabe BE C D Link Pairs Link Adjacent Groups E Mark Wells F UnMark Plate Outlier 5 Sample Names Group Mames H Figure 4 4 Well grid pop up menu Right click a well to display the pop up menu MasterPlex EX www miraibio
49. e application type and the dimensions for the virtual plate Type MasterPlex EX Rows Columns OK b Cancel Figure 4 35 Plate Wizard Plate Dimensions tab 3 Select an application module then enter the number of rows and columns for the virtual plate Click OK A module window opens and displays the empty well grid of the virtual plate Figure 4 36 MasterPlex EX www miraibio com 54 CHA PTER4 DEFINING A PLATE G H Figure 4 36 Virtual plate Selecting Data from a Source Plate The virtual pipette copies aspirates data from user selected wells in a source plate and pastes dispenses the data into a virtual plate The virtual pipette copies all of the analyte data in a well including the computed analyte concentrations It remains loaded until you dispense or clear the pipette oF NOTE The data source plates must contain the same type and number of analytes otherwise concentrations cannot be calculated If the source plates contain the same number of analytes but they are named differently use the virtual analyte filter to rename analytes so that the nomenclature is consistent See Working with the Virtual Analyte Filter on section 4 8 1 In the source plate select the wells of interest To select adjacent wells press and hold the mouse button while you drag the mouse pointer to select the wells of interest oF NOTE Selecting non adjacent wells is not recommended
50. eeeefs 50 Creating a Virtual Plate Sees 54 Working with the Virtual Analyte Filter 7707 59 Changing the Analyte Name eeeMMeRReHeeeee e e e e fe 62 Quality Control Manager optional module 63 CHAPTER 5 Normalization amp Fold Change Dashboard tab Go to Dashboard tab eiae erbe RR EAR UD ERO KO OR RCROE UR 67 Checking the Data Distributions Using Multi Charts err 68 Normalization and Fold Change 777760008 74 CHAPTER 6 Reviewing Data Data tab Add Of Delete the Column Pied 77 Sort or Filter the Column Dat eee 79 Exporting a Data Ria E VERENA GEO d NE ab DA ERA ERE AC EC Sl Printing Data eeeeMM eeeeeeee 83 CHAPTER 7 Data Charts Chart tab Viewing a Data Chart emm QA Chart Format rnm 8S8 Analyte Selector m g9 Changing Color Palette 9 Changing Chart Properties 02 Chart Template emm 04 Printing a Chart eme 99 Copying or Saving Chart Image ve 100 MasterPlex EX www miraibio com II CHAPTER 8 Export Data Export Manager tab Importing a User Defined Stylesheet veteet 102 Exporting a User Defined Stylesheet verece 103 Delete Stylesheet File from Style Sheet List 104 Viewing Original Data 105 Transform Original Data into Your Customized Data rer 106 APPENDIX A Preferences Grid Customize Menu MM 107 Print Preview Menu mn l 14 APPENDIX B MasterPlex EX Toolbars Main File Menu and Toolbar eee eT eT eT eer
51. el a Align to Center Align all headers footers to the center level ali Align to Bottom Align all headers footers to the bottom level Font Open font dialog for the header and footer font Insert Water Mark To insert water marks into your printing document open Water Mark dialog Figure A 12 There are two types of watermarks you can insert in your document one is Text and another is Picture They are separated into two tabs To insert a text watermark use Text Watermark tab To insert a picture watermark use the Picture Watermark tab Master Plex EX www miraibio com 117 APPENDIXA PREFERENCES Watermark Text Watermark freien piomien Text Direction Fo Font Transparency 0 255 In front All Pages IB Behind Enter page numbers and or page ranges pie separated by commas For example 1 3 5 12 Clear All Figure A 12 Watermark dialog Table A 6 Text Watermark properties Property Function Text Input text word in the text box or select predefined words from the drop down list Predefined words ASAP CONFIDENTIAL COPY DO NOT COPY DRAFT EVALUATION ORIGINAL PERSONAL SAMPLE TOP SECRET URGENT Direction Select text direction from one of the followings Horizontal Vertical BackwardDiagonal ForwardDiagonal Color Open color picker and choose text font color Font Open font dialog and choose text font Size Specify text font size Transparency Set transparency for the ins
52. ert text Position Select text position In front or Behind Page Range Set page range for the text water mark MasterPlex EX www miraibio com 118 APPENDIXA PREFERENCES Table A 7 Picture Watermark properties Property Load image Size mode Horizontal alignment Vertical alignment Tiling Transparency Position Page Range Function Open file open dialog and specify the image file to be inserted Select one of the size mode from followings Clip Insert the image as same size as original 1mage Stretch Stretch the image to horizontal direction Zoom Zoom the image to the page Set horizontal alignment left center or right Set vertical alignment left center or right Fill up the page by the 1mage Set transparency for the insert image Select image position In front or Behind Set page range for the image water mark MasterPlex EX www miraibio com 119 APPENDIXA PREFERENCES 4 but 2 10111 Ad Background 1 41 00 am 183 10194 8427 81 Standard 1 i0515 00 237039 208 1042940 284314 ci Standard 1 6152 00 297033 225 4908 06 233 14 Di Santerd 1 310400 297033 23 2557 05 284114 E Standard 1 1040 00 237039 381 121188 294114 Fi Standard 1 z 200 297035 i55 500 54 23 141 Gi Stendand 1 108 50 297039 190 345 86 2843 18 Hi Fanii 1 5500 292033 183 20336 29 31
53. ful and flexible tool for presenting and exporting your data Compared to regular report Custom report has greater flexibility on what and how to present data While EX stores its analysis results in an XML format document it is possible for users to present their data in whatever format they want The only thing users need to do is to define their presenting formats in XSL files Extensive Stylesheet Language Figure 8 1 Export Manager tab itp Ero nd a Rare Hz 12 rata rna TL Pad Teac I es PIN Quint Faber rr Satine a FEET ETET ue ee Eirean i Le dabat Et b Deiete U mens Cru F ACE MasterPlex EX www miraibio com 101 CHAPTERS EXPORT DATA 8 1 Importing a User Defined Stylesheet 1 Click Import button m The file open dialog appears Figure 8 2 Look in 3 examples all_csv xsl 4e norm xml xsl My Recent a jall xml xsl Documents iE first analyte html xsl 27 i conc unk xml xsl E Js all html xsl L esktop data n My Documents My Computer File name Open My Network Files of type MasterPlex Template xsl Figure 8 2 Open File Dialog 2 Select the file you want to import to the export manager c Style sheet s name is displayed in the Style Sheet list and XSL Information window shows style sheet s information Figure 8 3 MasterPlex EX www miraibio com 102 Report Template X fez 5x12 plate map HTML Eq Custom data format2 Custom da
54. he media damaged by accident abuse or misapplication THE ABOVE WARRANTIES ARE EXCLUSIVE AND IN LIEU OF ALL OTHER MasterPlex EX www miraibio com 11 LICENSE AGREEMENT WARRANTIES WHETHER EXPRESS OR IMPLIED INCLUDING THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE NO ORAL OR WRITTEN INFORMATION OR ADVICE GIVEN BY HISAL ITS EMPLOYEES DISTRIBUTORS OR AGENTS SHALL INCREASE THE SCOPE OF THE ABOVE WARRANTIES OR CREATE ANY NEW WARRANTIES SOME STATES DO NOT ALLOW THE EXCLUSION OF IMPLIED WARRANTIES SO THE ABOVE EXCLUSION MAY NOT APPLY TO YOU IN THAT EVENT ANY IMPLIED WARRANTIES ARE LIMITED IN DURATION TO NINETY 90 DAYS FROM THE DATE OF DELIVERY OF THE SOFTWARE THIS WARRANTY GIVES YOU SPECIFIC LEGAL RIGHTS YOU MAY HAVE OTHER RIGHTS WHICH VARY FROM STATE TO STATE LIMITATIONS OF REMEDIES HISAL s entire liability to you and your exclusive remedy shall be the replacement of the Software media or the refund of your purchase price as set forth above If HISAL or the HISAL s distributors are unable to deliver replacement media which is free of defects in materials and workmanship you may terminate this Agreement by returning the Software and your money will be refunded REGARDLESS OF WHETHER ANY REMEDY SET FORTH HEREIN FAILS ITS ESSENTIAL PURPOSE IN NO EVENT WILL HISAL BE LIABLE TO YOU FOR ANY DAMAGES INCLUDING ANY LOST PROFITS LOST DATA OR OTHER INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF TH
55. he results data Figure 3 3 Analytes Plate View Pane Figure 3 3 Plate tab displaying results data MasterPlex EX www miraibio com 14 CHAPTER3 GETTING STARTED 3 4 Import csv xls or Open Ixd mlx Files by drag and drop 1 Open Windows Explorer and adjust the window size so that you can view both the MasterPlex EX and Windows Explorer application windows 2 Use Windows Explorer to navigate to the csv xls Ixd or mlx file s that you want to open 3 Select the file s of interest then click and hold the mouse button while you drag the selected file s to the MasterPlex application menu bar area Figure 3 4 To select adjacent files press and hold the Shift key while you click the first and last file in the selection To select nonadjacent files press and hold the Ctrl key while you click the files of interest 4 Release the mouse button The file s open in MasterPlex EX
56. icate View chart MasterPlex EX www miraibio com 87 CHAPTER7 DATA CHARTS 7 2 Chart Format MasterPlex EX provides various chart formats Table 7 3 To change a chart format for the selected well data click the Chart Gallery button E and make a selection from the drop down list of Chart Gallery Table 7 3 Available chart format Icon Features Bar style x y chart 3D bar style x y chart 3D bar style x y z chart Point Point style x y chart Line interpolated style x y chart Step line interpolated style x y chart Spline interpolated style x y chart 3D line interpolated style x y chart Step Line 3D 3D step line interpolated style x y chart Spline 3D 3D spline interpolated style x y chart Are painted style x y chart Spline area painted style x y chart 3D area painted style x y chart Spline Area 3D 3D spline area style x y chart Pie Pie style circular chart 3D pie style circular chart Doughnut style circular chart 3D doughnut style circular chart Line interpolated style radar chart Point plotted style radar chart Peo6eeceEk Mer EER ek MasterPlex EX www miraibio com 88 CHAPTER7 DATA CHARTS 7 3 Analyte Selector In the Well Group chart Analyte Selector allows you to change the analytes position in the chart and allows you to display on off setting for each analyte To move the analyte position ED 1 Click Analyte Selector icon Analyte selector drop down list appears Figure 7 6 2 Select
57. in license information dialog Tools User Open user management dialog For 21 CFR Part 11 module only Open log viewer For 21 CFR Part 11 module only Open verification checker dialog For 21 CFR Part 11 module only Open video tutorial Open support URL by the default browser Management Tools Log Viewer Tools gt Verify files Help Tutorial Help Online Support Help About Display splash screen with application version information Look and Feel Change application skins B 2 Plate Tab Toolbar The Plate tab toolbar is available on the top of the well grid in the plate tab 3 Figure B 2 Plate toolbar Table B 2 Plate toolbar buttons and functions Menu Bar Toolbar Function Command Icon Background B Mark selected wells as Background Control B Mark selected wells as Control MasterPlex EX www miraibio com 122 APPENDIXB MASTERPLEX EX TOOLBARS Treatment Mark selected wells as Treatment Unmark a Unmark selected wells Subtract L3 Toggle subtract background function Background bA Link One vs Link between one control group and multiple Multi treatment group Link adjacent Link adjacent control groups and treatment multiples groups Auto Fill Open Auto Fill dialog Quality Control EF Open Quality Control Manager Manager Optional module Template Open template manager Manager Plate Open plate preference dialog Preferences B 3 Data Table Tab Toolbar The Data Table too
58. ins ownership of all copies of the Software itself LICENSE You may a Use the Software on a single machine at any given time b Obtain limited numbers of Copy Protection Devices Additional Copy Protection Devices are provided only as a convenience of running the software c In no manner engineer or reverse engineer the copy protection hardware or whole or part of the software d Copy the software only for backup provided that you reproduce all copyright and other proprietary notices that are on the original copy of the Software provided to you Certain Software however may include mechanisms to limit or inhibit copying Such Software is marked copy protected e Transfer of the Software and all rights under this Agreement to another party together with a copy of this Agreement if the other party agrees to accept the terms and conditions of this Agreement If you transfer the Software you must at the same time either transfer all MasterPlex EX www miraibio com LICENSE AGREEMENT copies whether in printed or machine readable form to the same party or destroy and copies not transferred RESTRICTIONS You may not use copy modify or transfer the Software or any copy in whole or in part except as expressly provided for in this Agreement Any attempt to transfer any of the rights duties or obligations hereunder except as expressly provided for in this Agreement is void YOU MAY NOT RENT LEASE LOAN RESELL FOR PROFI
59. ions Manual Use Raw MFI count Normalized MFI or Fold Change value for threshold conditions Figure 4 50 Manual Extrapalated Values The wells outside Lower Upper of this range are flagged v Response Values 150 Calculated Values re Combination selection is allowed b Apply Figure 4 50 Outlier check boxes LLOD Lower Limit of Detection Flag the lower values than the LLOD calculation value Figure 4 51 LLOD is based on the MFI mean value of the selected wells plus the standard deviation multiplied by the user selected number For all analytes Select the base v Calculate LLOD MFI wells from Fa op up well grid Ivf Exclude selected wells from outlier pas pop up g Select wells to be used in LLOD calculation LLOD 2 Mean MFI of selected wells E Stdey Figure 4 51 Outlier check boxes i MasterPlex EX www miraibio com 65 CHA PTER4 DEFINING A PLATE ULOD Upper Limit of Detection Flag the upper values than the ULOD calculation value Figure 4 45 ULOD is based on the MFI mean value of the selected wells plus the standard deviation multiplied by the user selected number Extrapolated Values Manual Select the base For all analytes MFI wells from f Calculate LILOD pop up well grid Exclude selected wells from outlier marking Select wells to be used in ULOD calculation ULOD Mean MFI of selected wells eo Stdev
60. k select other wells to exit the edit mode Figure 4 21 Figure 4 21 Flag the data manually Set multiple outlier flag using batch flagging feature 2 Select multiple wells you want to set the dilution at one time Figure 4 22 MasterPlex EX www miraibio com 42 CHAPTERA DEFINING A PLATE Outlier a oi false Figure 4 22 Flagging outlier 2 Right click on the well grid Context menu appears Figure 4 23 3 f ADI LT Aspirate Dispense Clear Mark Wells Unmark Auta Fill Flate Dilution F E LA Set Far all analytes Set for current analyte Unset For all analytes Unset For current analyte Figure 4 23 Batch outlier flagging menus 3 Select Plate Outlier menu Sub menu appears Figure 4 23 4 Select one of the sub menu to flag the data Check box status is changed by the selected menu Figure 4 24 MasterPlex EX www miraibio com 43 CHA PTER4 DEFINING A PLATE Figure 4 24 Flagged out data MasterPlex EX www miraibio com 44 CHA PTER4 DEFINING A PLATE 4 6 Working With Templates A plate definition includes Well types and well groups Housekeeping gene status Links between the control s and well groups Data calculated for the plate for example normalization MFI or fold changes Data manually entered in the plate for example sample names or sample amount You can save the plate definition as a template You can apply a template to an ac
61. late You can apply a template to an active chart Templates may also be exported imported or deleted Opening the Chart Template Manager 1 Click the Chart Template Manager button aly The Chart Template Manager appears Figure 7 12 2 Click a chart template in the Available Templates list to view information about the template Template Manager x Available Templates Template Properties m My favorite Name y analyte x MFI black mxtc e y analyte x MFI black id Created by Creation date 9 24 2009 Creation time 10 53 16 AM Description Load h Save j Export l Import Overwrite Delete 1 Close Figure 7 12 Chart Template Manager shows available templates Click a template to view information about the template Saving a Chart Template You can save the current chart properties to a template 1 After you have finished modifying the properties open the Chart Template Manager and click the Save button The Template Name box appears Figure 7 13 MasterPlex EX www miraibio com 94 CHAPTER7 DATA CHARTS Template Information Mame Description Cancel Figure 7 13 Template Name and Description box 2 Enter a name for the template and click OK The new template is added to the Available Template list Loading a Template You can apply or oad a saved template to the current chart 1 In the Template Manager select the template that you want to apply to the chart
62. lbar is available on the top of the data grid in the Data Table tab Show Column Selector Export to File Ee Print Preview Er Table Template Figure B 4 Calculation toolbar MasterPlex EX www miraibio com 123 APPENDIXB MASTERPLEX EX TOOLBARS Table B 4 Calculation toolbar buttons and functions Menu Bar Function Command Button Show Hide Columns Show or hide columns selector Selector m Export to File e Export data table by selected format Format Excel CSV PDF HTML Text Print Preview Open print preview window Table Template Open table template dialog MasterPlex EX www miraibio com 124 APPENDIXB MASTERPLEX EX TOOLBARS B 4 Chart Tab Toolbar The chart toolbar 1s available on the top of the chart view area in the chart tab algo aou Figure B 5 Chart toolbar Table B 5 Chart toolbar buttons and functions Menu Bar Toolbar Function Command Button Replicate View Analyte Selector Shows drop down list for all analytes Well Selector Toggle replicate view mode Shows mini sized plate view eee Shows drop down list of available chart format Chart Gallery Color Palette Shows drop down list of available palette Chart Properties Chart Template m Open chart template manager m Print Preview Open print preview Open chart properties dialog MasterPlex EX www miraibio com 125 APPENDIXB MASTERPLEX EX TOOLBARS B 5 Export Manager Tab Toolbar The Expor
63. le Windows Tool Help Look And Feel Logged onas Figure 3 1 MasterPlex user interface MasterPlex EX www miraibio com 12 CHAPTER3 GETTING STARTED 3 3 Importing Luminex Results To begin a MasterPlex EX analysis import a csv xls or Ixd file from the Luminex 100 200 or BioPlex system using toolbar menu bar or application icon oF NOTE The Luminex default directory is named Output Importing Luminex Results Using the File Open Menu File Open Icon or Application Icon 1 Choose File gt Open click the File Open icon he or click the application p icon P9 c The Open dialog box appears Figure 3 2 2 Enter the file path for the csv xls or Ixd that you want to import Look in I3 examples A E 4 Bh H10Plex csv My Recent ASRJILS cev Documents Desktop n My Documents My Computer em LP File name My Network Filesoftype Data Files csv xls led mb Figure 3 2 Open dialog box MasterPlex EX www miraibio com 13 CHAPTER3 GETTING STARTED 3 Navigate to the directory of the csv xls or Ixd that you want to import 4 Select one or more csv xls or Ixd files and click Open To select adjacent files press and hold the Shift key while you click the first and last file in the selection To select nonadjacent files press and hold the Ctrl key while you click the files of interest The EX module window opens and displays t
64. lecy 0 constddey 0 conayg 0 concv g normfi resulthdrz z lt Bead id 2 mfi 103 conc 0 count 124 status 1 constr resstddev 0 Figure 8 6 Confirmation Dialog I lt MasterPlex EX www miraibio com 105 CHAPTERS EXPORT DATA 2 To save this data click the Save button 3 To print this data click the Print button 8 5 Transform Original Data into Your Customized Data 1 Select the style sheet you want to apply from the style sheet list 2 Click the Apply button j The transformed data is shown in the preview window Figure 8 7 P Save Pm Print lis Flat File by Determination FileName RunDate RunTime SampleWell AnalyteName WellType SampleName C Documents and i Settings tshimizu Desktop examples H 1OPlex csv Insee xen one GM CSF Other 4 C Documents and Settings tshrmizu Desktop examples H 1 OPlex csv C Documents and Settings tshimizu Desktop examples H10Plex css C Documents and 9 12 2008 8 10 PM Al IFN gamma Other l D 12 2008 8 10 PM Al Il 1 Beta Other 4 Settings tshimizu Desktop examples H10Plex csv RARI a is IL 10 Other PERT ER Plex csv 9 12 2008 8 10 PM Al IL 2 Other senior RN NEN Plex csv abanico ras IL 4 Other 3 ee ee Plex csv Tre i i Hen IL 5 Other 8 priino RN Plex csv EDU ENS rn IL 6 Other l E eee Plex csv m en IL 8 Other 3 ee eee Plex csv MAAARI ES i TNF alpha Other 2 C Documents and 120008 10 PM Ri a C amp E
65. lex EX www miraibio com 59 CHA PTER4 DEFINING A PLATE Virtual Analyte Filter New Analytes Assign Aliases EGMCSF Click here to assign IFN gamma Click here to assign Il 1 Beta Click here to assign IL 10 Click here to assign IL 2 Click here to assign IL 4 Click here to assign IL 5 Click here to assign IL 6 Click here to assign IL 8 Click here to assign TNF alpha Click here to assign Check all analytes Add all as new OK Cancel Figure 4 42 Virtual analyte filter shows the analytes in the virtual pipette Selecting and Renaming Analytes If the virtual analyte filter appears you must select and 1f necessary rename the analytes to match the number and names of the analytes in the virtual plate 1 In the virtual analyte filter Figure 4 44 place a check mark next to each analyte that you want to add to the virtual plate To select all analytes for the virtual plate click Check All 2 To rename an analyte so that it is consistent with the nomenclature in the virtual plate a Click here to assign next to the analyte that you want to rename A drop down list shows the names of the analytes in the virtual plate Figure 4 43 b Select a name from the drop down list The virtual analyte filter displays the new name for the analyte MasterPlex EX www miraibio com 60 CHA PTER4 DEFINING A PLATE Virtual Analyte Filter New Analytes Assign Aliases GM CSF Click here to assign IFM g
66. lick Export to File drop down button 2 Select the file format you want to export There are five file formats available Excel CSV PDF HTML and Text Figure 6 8 Text Figure 6 8 Export to File menu 3 File save dialog appears Set file path and input file name then click OK Figure 6 9 Figure 6 9 File save dialog MasterPlex EX www miraibio com 81 CHAPTER6 REVIEWING DATA 4 After saving the file an Open file prompt appears Figure 6 10 If you want to open the saved file immediately using the program the files extension is associated with click Yes The saved file is opened on the program Figure 6 11 E Microsoft Excol Bata Taber xis Wt BW pe pei Peet xk d s ies te PRSE UR 8 E Toresa E we mi s E 3 Hs a so ou LH Di D E Di Bi i 434 a Y 934 G a 34 4 4 34 4 343 434 4 44 Se 734 853 3 i i c mem m mdi o a auum Ea mF Di f i ela lel lim b D a D Moak Hn Shoe bul Figure 6 11 Opening in Excel MasterPlex EX www miraibio com 82 CHAPTER6 REVIEWING DATA 6 4 Printing a Data You can preview your data with the Print Preview button 1 Click the Print Preview button Print preview window appears Figure 6 12 File View Background eem ons Name GM CSF a Standard 1 108 50 2970 39 190 Standard 1 56 00 2970 38 L Standard 1 10034 50 2970 38 o 452 E re
67. ll MasterPlex to C Program Files Hitachisoft MasterPlex Figure 2 2 Destination Folder screen To specify a different destination folder click Change choose the folder and click Next Figure 2 2 3 To continue click Next Custom module setup window appears Figure 2 3 MasterPlex EX www miraibio com 5 CHAPTER2 INSTALLING MASTERPLEX iz MasterPlex InstallShield Wizard Custom Setup Select the program features you want installed Click on an icon in the list below to change how a feature is installed Feature Description um FSi masterPlex r ise The application platform E ReaderFit This feature requires 1044KB on your hard drive It has 3of3 subfeatures selected The subfeatures require 2824KB on your hard drive Cancel Figure 2 3 Module selection window 4 Make sure the module name you purchased and click amp 1 icon you don t want to install Ea run meshudniiks Jh i im miere Inmsiallseid Wirarid Cus ns Taetug Cusi faetum Jeri Hm popanfasra yen rear nua gaz t bhe pogan adua pou rear mia Click an mkonn He lat baa in changa hore afarira gi iracaled Cik an anicpnin He bet bakes be charga heri afarira u iracaled remus Reni nr Pasture Dezariprian j i i EI Mhir berra riba raed onia herd crea GE Thufaacurm arci al riaria oil be eed an kea hard deren Figure 2 4 Install module selection window MasterPlex EX www miraibio com 6 CHAPTER2 INSTAL
68. munere to group by that column teaa Na eem DUN NUS m e a GM CSF Bad Bead Name i B1 GM CSF Star Conc CV sal LE Conc Stdev Dilution Group Mame A1 Background 1 Bi Standard 1 Ci Standard 1 Di Standard 1 apmus co es EN Lg nt A Li Well Group PPE EP PO TEETH ere EP PVP pirer RRA SE gt FEL Bead Name GMECSE eas hh essersi E Dont ees a Al Background 1 _ amp Group Name Background 1 Ri Standard 1 Al 43 AZ 3t _ amp Group Name Standard 1 Bi 1051 Ctl 615z Figure A 4 Multi Group by Drag amp Drop MasterPlex EX www miraibio com 109 APPENDIXA PREFERENCES Group Box Menu Group Box has context menu Table A 2 shows the menus Table A 2 Main toolbar buttons and functions Icon Command Function Expand all group trees s E Full Collapse Collapse all group trees Se Clear Grouping Clear group and return the group columns to the grid column Working with Column Filter There are two ways to set a filter The first way 1s by using the filter drop down menu from the column Figure A 5 You can filter the column by selecting the specific data in the column The second way is by using the Filter Builder window Figure A 6 Well Sample Name Well Sample Name El Bead Name GM CSF LEl Bead Name GM CSF Al A 10 B1 C1 I Bead Name IFN gamma A10 EJ Bead Mame Il 1 Beta A10 Figure A 5 Direct Filtering from the column MasterPle
69. n Control Treatment Display all treatments distributions which belong one Chart control group Figure 5 1 Well Chart Plot MFI and normalized MFI simultaneously Figure 5 1 Analyte Comparison Plot all data points between two analytes Figure 5 1 Sample MFI Correlation plot between sample amount and MFI Comparison Figure 5 1 MasterPlex EX www miraibio com 68 CHAPTER5 NORMALIZATION amp FOLD CHANGE Control Treatment Chart Control Treatment Chart plots all treatments data belong one control group with an error bar Figure 5 3 All control groups and treatments are plotted on the chart at the same time Chart can be copied or exported from context menu and display data type can be chosen from context menu as well Figure 5 4 Control Treatment 1400 ACTS 1200 1000 800 500 400 200 Cil 1 Cil 2 Ctrl 3 Ctrl 4 Cil 5 Cil 6 1400 Lal Lu Li B ACTB MI 1200 if 1000 B00 a ESET Export 600 w Display MFI 400 Display Normalized MFI 200 Ctrl 1 Ctl 2 Ctrl 3 Ctl 4 Ctr 5 Ctrl 6 Figure 5 4 Context menu for Control Treatment Chart MasterPlex EX www miraibio com 69 CHAPTER5 NORMALIZATION amp FOLD CHANGE Well Chart Well chart plots MFI and normalized MFI data selected by the mini plate selection tool Figure 5 5 Chart can be copied or exported from context menu and MFI and normalized MFI data can be tuned off from context menu as well
70. perator Cs Filter Builder add remove conditions and groups of To add filter condition click button Sample Mame Begins with enter a value conditions To remove filter condition QD And click x button Or aD Mot And QD Not Or Add Condition Add Group Clear All Figure A 8 Filter Builder Window 3 Click Sample Name and choose one of the column item 4 Click Equals and choose one of the operator Table A 3 shows the conditions you can choose from 5 Click lt Enter a value gt and enter the operand value 6 Click the Apply button to apply the filter setting to the grid If you want to apply and close the Filter Builder window click the OK button Table A 3 Available Commands for Filter Icon Operator Function Shows only Sample Name lt value gt Does not equal Shows only Sample Name value Is greater than Shows only Sample Name gt lt value gt Is greater than or equal Shows Sample Name lt value gt and Sample Name gt lt value gt lt Shows only Sample Name lt lt value gt Is less than or equal Shows Sample Name lt value gt and Sample Name lt lt value gt MasterPlex EX www miraibio com 112 APPENDIXA PREFERENCES Is between Shows only the value which has between first value and second value iz Is not between Shows only the outside value which has between first lt value gt and second l
71. plate unusable Importing a Template You can import a template mxte from a user specified location 1 In the Template Manager click Import button The Open dialog box appears Figure 4 29 Look in I3 examples gt e m sample name empty La data My Recent Documents Desktop My Documents 48 My Computer File name Open My Network Files of type MasterFlex Template matq Cancel Figure 4 29 Open dialog box 2 Choose the directory with the template that you want to import 3 Select the template and click Open The template name is added to the Template Manager Deleting a Template You can delete a template mxte from the system 1 In the Template Manager click the template that you want to delete 2 Click Delete button MasterPlex EX www miraibio com 48 CHA PTER4 DEFINING A PLATE A confirmation box appears Figure 4 30 Warning x A Are you sure you want to delete Mb5PlexSingleStd Figure 4 30 Confirmation box 3 Click OK to delete the template The template is removed from the Template Manager WARNING This permanently removes the template from the system WARNING MasterPlex EX www miraibio com 49 CHA PTER4 DEFINING A PLATE 4 7 Preferences Preferences are user modifiable software settings They are displayed in the Preferences dialog box To open the Preferences dialog box Figure 4 31 click the Preferences button i
72. ply to the plate 2 Click the Load button The template is applied and the well grid shows the new well attributes well type well group and links to standard data sets Overwriting a Template You can overwrite an existing template with the current plate definition 1 In the Template Manager select the template that you want to overwrite 2 Click the Overwrite button A confirmation box appears Figure 4 27 MasterPlex EX www miraibio com 46 CHA PTER4 DEFINING A PLATE Warning x Ay Are you sure you want to overwrite M5PlexSinglestd Cancel Figure 4 27 Confirmation box 1 Click OK to overwrite the selected template with the current plate definition Exporting a Template You can export a template to a user specified location 1 In the Template Manager click the template you want to export 2 Click the Export button The Save As dialog box appears Figure 4 28 Save in _ examples 2 i sample name empty Et data My Recent Documents Desktop My Documents 3 My Computer q a a My Network Saveastype MasterPlex Template mda v Figure 4 28 Save As dialog box 3 Choose the directory for the template that you want to export MasterPlex EX www miraibio com AT CHA PTER4 DEFINING A PLATE 4 Enter a name for the template mxte dr NOTE A template must have a mxte file extension Changing the extension will render the exported tem
73. raibio com 63 CHAPTERA DEFINING A PLATE specified threshold with a red border Figure 4 48 To set a threshold s 1 Select analytes you want to attach the threshold criteria from the analyte pane Use All analytes check box or Ctrl key for multiple selection 2 Check Show threshold marker box and or Mark as outlier box 3 Select the threshold criterion from the threshold tab 4 Set threshold conditions and click apply button Close the dialog box A red border marks wells that contain data meet the threshold criteria If you choose Mark as outlier at the same time the data are marked as outlier and outlier check boxes are checked Figure 4 49 4 5 6 i 8 9 10 1 2 3 112 00 92 00 2426 50 43 00 36 00 80 00 10516 00 4911 00 106 50 186 00 i 6152 00 6299 00 39 00 5011 00 43 00 38 00 40 00 45 00 3104 00 2990 50 5591 00 3989 50 113 00 38 00 44 00 40 00 wt 1094 00 45 00 1808 00 270 00 49 00 40 00 36 00 47 00 300 00 39 00 1129 00 42 00 40 00 37 00 49 00 ppm ine enl inv enl 111 nn 7n nn Aq nal n nn nC nal Figure 4 48 Well grid dL JL d LL d JL i M Imm Figure 4 49 Outlier check boxes MasterPlex EX www miraibio com 64 CHA PTERA DEFINING A PLATE Settings Flag wells outside Show red rectangle indicator inside the grid 1f the range threshold conditions meet the criteria Mark as outlier Mark flagged data as outlier Threshold Opt
74. rl 1 Ctrl 1 Ctrl 1 cil ci Ctrl 1 Ctrl 1 Ctrl 1 Ctrl 1 Ctrl 1 Ctrl 1 Figure 4 17 7 Display linking status MasterPlex EX www miraibio com 40 CHA PTER4 DEFINING A PLATE 4 4 Attach Housekeeping Gene Status If you need to set housekeeping gene status to some analyte for normalization you can attach the housekeeping gene status to the analyte 1 Right click on the analyte name you want to add housekeeping gene status in the analyte pane Context menu appears Figure 4 18 House Keeping Gene Rename ACTB Figure 4 18 Context menu for analyte pane 2 Select House Keeping Gene menu from the context menu Analyte icon in front of the analyte name turns red to green Figure 4 19 A co M CXCLO A dA GAPD F Won Figure 4 19 Attach housekeeping gene status 3 Repeat step 1 and 2 until all house keeping genes have housekeeping gene status MasterPlex EX www miraibio com 41 CHA PTER4 DEFINING A PLATE 4 5 Flagging the data If you need to set outlier flag due to our of range results you can flag the data as outlier Set outlier flag manually 1 Select Outlier data type from upper drop down list or lower drop down list Figure 4 20 Current outlier status are shown in the plate well grid Sela i mammas T m Figure 4 20 Display outlier status 2 Select a well you want to flag gt click same well to enter the edit mode gt click once again to make a chec
75. s MasterPlex EX software analyzes results files csv xls or Ixd from the Luminex 100 200 or BioPlex system The analysis steps include Import a Luminex results file csv xls or Ixd Designate well types control treatment or background and well groups Attach housekeeping gene status to the analytes Associate or ink a control group set to an treatment group s Normalization and compute fold change Save the Luminex results file in MasterPlex EX file format mlxe The mlxe file includes information associated with the file for example well definitions and calculated results After the fold changes are calculated you can View the results in graphs or several different report formats Create a virtual plate a simulated microtiter plate that contains data from user selected actual plates csv xls Ixd or mlx MasterPlex EX www miraibio com 11 CHAPTER3 GETTING STARTED 3 2 Starting MasterPlex EX On the desk top double click the MasterPlex icon A Alternatively you can click the Windows start menu button and select Programs gt MasterPlex 2010 gt MasterPlex 2010 The MasterPlex user interface appears and lists up all detected modules in the application pane Figure 3 1 You can import a Luminex or BioPlex results file csv xls or Ixd or create a virtual plate from this interface For more information on virtual plates see Chapter 4 Section 4 7 Creating a Virtual Plate a MasterPlex F
76. s a step format to explain the various tasks associated with MasterPlex EX A symbol may follow a step instruction It indicates the software response to the action performed by the user MasterPlex EX www miraibio com 1 CHAPTER 1 WELCOME Screen Captures Screen captures may accompany the step instructions for further illustration The screen captures in this manual may not exactly match those displayed on your screen 1 2 Technical Support You can contact MiraiBio Technical support at Hitachi Software Engineering America Ltd 601 Gateway Boulevard Suite 100 South San Francisco CA 94080 USA Tel 1 650 615 7600 Toll Free 1 888 615 9600 Fax 1 650 615 7639 E mail support miraibio com www miraibio com MasterPlex EX www miraibio com 2 CHAPTER2 INSTALLING MASTERPLEX CHAPTER 2 Installing MasterPlex This chapter explains the minimum hardware and software requirements needed to install and use MasterPlex EX It provides installation instructions for a computer connected to the Luminex 100 200 or BioPlex system 2 1 Requirements For optimum performance MasterPlex EX requires hardware and software that meet or exceed the following specifications It 1s also strongly recommended that you use the Luminex XY platform Minimum Hardware Requirements Platform CPU Intel Pentium 4 2 GHz or equivalent Intel Pentium 4 2 GHz or better recommended Storage space 120 MB available hard drive space
77. s data Figure 3 11 ol 4duduts E EDEDO i es iW Count 202 Lid tinis SS E SSS ACTB i 5 A ca 1168 00 3 00 31 00 218 00 2 00 6 00 529 00 513 00 A oc I x 3 m 9 o 5 3 z2 2 1756 de ICAM1 1280 00 4 00 36 00 248 50 2 00 7 00 553 00 600 00 i B B nn ce ore a EEUERUR mmm mim mu greek 2 2 au ELLA Tc azzzzmicxepiIded oriens ot EMI a a per A amp FNG 227 186 209 168 199 207 229 233 B MAPKS 289 50 2 00 7 00 67 00 2 00 3 00 486 50 340 50 C pee 2 pee M MMMM eee LASS A A UE eM ie TGFBI 200 236 246 187 218 196 190 206 d TF L 4 i t li J br 28450 2 00 11 00 66 00 2 00 3 00 607 50 377 00 gt Sees E e Tee pends E eee rM LE e E 232 201 182 172 219 184 224 162 6400 643 00 3 00 18 0 151 00 3 00 340 00 3 00 Figure 3 11 Plate Map tab MasterPlex EX www miraibio com 24 CHA PTER4 DEFINING A PLATE 4 Defining a Plate Plate tab After you import a Luminex results file csv xls xd your analysis begins by defining a plate This chapter explains how to define and save a plate The steps to define a plate include Designate well type to identify the standard unknown background and control wells Attach Housekeeping gene status by right clicking on the analyte pane A plate can ha
78. t Manager toolbar 1s available on the top of the preview area in the export manager tab Figure B 5 Chart toolbar Table B 6 Chart toolbar buttons and functions Menu Bar Toolbar Function Command Button Print s Print current displayed document MasterPlex EX www miraibio com 126
79. t value gt abc Contains Shows only the value contains lt value gt acb Does not contain Shows only the value does not contains lt value gt alb Begins with Shows only the value starts with lt value gt Shows only the value ends with lt value gt Shows only Sample Name gt lt value gt Shows only Sample Name gt lt value gt Shows only value are blank Shows only value are not blank Ooo Is any of Shows only value which has lt value gt s rr p 3 ra ke Shows only value does not have lt value gt s Well Group Name MFI Fi Standard 1 292 00 Bead Name Equals GM CSF pe 2 Standar 300 MFI Is between 200 00 and 500 00 E6 Unknown 1 270 00 Bead Name Equals IL 10 ee bt sini MFI Is between 500 00 and 1000 00 SJ Bead Mame IL 10 Hi Standard 1 537 00 pm UK Cancel Apply H2 Standard 1 550 00 B3 Unknown 1 587 00 CL Shows only E4 Unknown 1 575 00 Bead name is GM CSF and MFI is between 200 and 500 B6 Unknown 1 621 50 or C7 Unknown 1 866 50 Bead name is IL 10 and MFI is between 500 and 1000 DF Unknown 1 511 00 A8 Unknown 1 fo 00 G amp Unknown 1 831 00 Figure A 9 Example of the complex filter criteria Master Plex EX www miraibio com 113 APPENDIXA PREFERENCES A 2 Print Preview Menu Print preview allows you to zoom navigate print out set printing options export and other useful tasks Figure A 10 Preview Menu Preview Toolbar
80. ta format1 Tab Format PlateFormat Report InFarmatian x Mame 812 plate map HTML Modified Time 1 11 2010 6 30 00 PM Qutput Method Html Figure 8 3 Open File Dialog 8 2 Exporting a User Defined Stylesheet Export 1 Click Export button The file save dialog appears Figure 8 4 CHAPTERS EXPORT DATA MasterPlex EX www miraibio com 103 CHAPTERS EXPORT DATA Save in 3 examples E a norm xml xsl My Recent a jall xml xsi Documents HE first_analyte_html xsl ye conc_unk_xmi xsl all_htrml xsl data File name My Netware _ Saveastype Masterlex Style Sheet x Figure 8 4 Open File Dialog 2 Set the destination and input file name then click the Save button Style sheet s name is displayed in the Style Sheet window and XSL Information window shows style sheet s information Figure 8 3 8 3 Delete Style Sheet File from Style Sheet List 1 Select the style sheet you want to delete from the style sheet list 2 Click the Delete button Delete l The confirmation dialog appears Figure 8 5 3 Click OK to delete MasterPlex EX www miraibio com 104 CHAPTERS EXPORT DATA Warning x Ay Are vou sure vou want to delete All HTML Figure 8 5 Confirmation Dialog 8 4 Viewing Original Data 1 Click View Original button V orignal Original data by xml format is displayed in the preview window Figure 8 6
81. that displays the well contents for the analyte selected from the Bead Set panel and data type selected from the data drop down list Some data types can be edited see Table 3 1 Select one of the wells The wells turn gray then click the same well once again to edit mode Shows the types of data available for display in the well grid Make a selection from this drop down list to choose the data type displayed in the well grid Click the drop down arrow to view the list and select a data type See Table 3 1 for a description of the data types The well grid can be separated into upper and lower grids by clicking lower grid switch See Figure 3 8 for more further details Enables the lower grid data selection and display Displays the selected data type value for the active selected well Displays a list of the analytes bead sets in an assay Icons for sample marking Displays the background subtracted value Icons for operating plate tab MasterPlex EX www miraibio com 20 CHAPTER3 GETTING STARTED Table 3 1 Data Types in the well grid Data Type Description Edit Data MFI Median The median fluorescence intensity measured Fluorescence by the Luminex 100 200 or BioPlex system for Intensity a bead set count Count The number of beads per bead set detected by the Luminex 100 200 or BioPlex system specified by the user in the Luminex software Sample Amount Yes Outlier A check mark indicates the well is o
82. the analyte you want to move 3 To move the analyte to the left click Up button To move the analyte to right click Down button The analyte moves one position to the left or right from its current position Figure 7 7 In the Single Analyte chart the Analyte Selector allows you to select the analyte you want to display in the chart Figure 7 8 IFN gamma All Analytes in the B i i Bela plate To turn the W IL 10 display of the IL 2 ff IL 4 analyte on or off 1 5 check the box next IL 6 to it ET TNF alpha Figure 7 6 Analyte Selector drop down list MasterPlex EX www miraibio com 89 CHAPTER7 DATA CHARTS F GM CSF IFN gamma E IFN gamma E GM CSF Il 1 Beta Select the analyte V 1 1 Beta ate and click the M IL 10 IL 2 Down button IL 2 IL 4 IL 4 IL 5 v IL 5 v IL 6 v IL 6 IL 8 IL 8 M TNF alpha v TNF alpha 12306 12000 N 12000 T 10516 LO000 10000 az19 anan Bun T T 6000 85000 4000 000 2000 2000 0 0 y IFN gamma Il 1 Beta Il IFM gamm a v3 Il 1 Beta Il Figure 7 7 Change the analyte position E GM CSF IFN gamma All Analytes in the I 1 Beta plate To select the analyte click the radio button next to the analyte name IL 10 7 na m E ch Py IL 5 E e E TNF alpha Figure 7 8 Analyte Selector drop down list MasterPlex EX www miraibio com 90 CHAPTER7 DA
83. tive plate Templates may also be exported imported or deleted Opening the Template Manager The Template Manager 1s a tool that helps you manage your templates 1 Click the Template Manager button The Template Manager appears Figure 4 25 2 Click a template in the Available Templates list to view information about the template Template Manager x Available Templates Template Properties Human 10plex Mame M5PlexSingleStd E M5PlexSingleStd Created by Creation date 9 3 2008 Creation time 9 59 45 pM Description Mouse 5 plex Single standard set eid m e sme aal n Export Import l Overwrite Delete Close Figure 4 25 Template Manager shows available templates Click a template to view information about the template MasterPlex EX www miraibio com 45 CHA PTER4 DEFINING A PLATE Saving a Template You can save the current plate definition to a template 1 After you have finished defining a plate open the Template Manager and click the Save button The Template Name and Description box appears Figure 4 26 Mame Description Cancel Figure 4 26 Template Name and Description box 2 Enter a name and descriptions for the template and click OK The new template is added to the Available Template list Loading a Template You can apply or oad a saved template to the current plate 1 In the Template Manager select the template that you want to ap
84. uminex 100 200 or BioPlex software To edit the analyst name enter a new name Plate Name Shows plate name of this file MasterPlex EX www miraibio com 51 CHA PTER4 DEFINING A PLATE Background type Average Calculate average value in the background group Background Bkg MFI Bkg MFI Bkg MFI t Bkg MFI n where n the number of background wells in the plate Peak Value Take highest value in the background group Lowest Value Take lowest value in the background group Outlier Options You can select one of the criteria for threshold marker from MFI Concentration Bead count and Error range Select one of them and enter an MFI count concentration or error range threshold for a plate The software automatically marks wells that contain data less than the user specified threshold with a red border Figure 4 34 To set a threshold s 1 Check Show threshold marker box 2 Check one of the radio button in front of the data type you want to use as a threshold marker 3 Select equity equal symbol and input the value in the box 4 Click Apply to reflect current setting to the plate or click OK to reflect and close the dialog box A red border marks wells that contain data less than or greater than threshold for all analyte Figure 4 25 MasterPlex EX www miraibio com 52 1 2 3 28 00 29 00 11083 00 10831 00 587 00 9072 00 8899 00 58 00 C 7044 00 7087 00 63 00 D 4987 00 4440 00 95 50 282
85. ution direction for the selected wells click a dilution direction arrow The gradient map shows the location and direction of the dilution gradient s Figure 4 12 Click an arrow to choose a dilution direction This gradient map specifies a separate dilution gradient in each column of the selected wells The starting value is at the top of a column This gradient map specifies selected wells The starting value is at the upper left well and the end concentration is at the lower right well Click an arrow to choose a dilution direction Figure 4 12 Example dilution gradient maps Click a dilution direction arrow to choose the dilution gradient configuration for the selected wells MasterPlex EX www miraibio com 35 CHA PTER4 DEFINING A PLATE 7 To specify the same starting value dilution factor and units for all analytes in the standard data set choose the Fill for all analytes option To specify a different starting value dilution factor or unit for a different analyte repeat step 2 through step 4 8 Click Apply button when finished entering the sample amount value the dilution and the dilution direction for all analytes in the selected wells If you want to close the dialog box at the same time click Fill amp Close button MasterPlex EX www miraibio com 36 CHA PTER4 DEFINING A PLATE Fill in for replicate samples If you have replicate samples in your plate and 1f you want to fill the same
86. utlier and Yes the well data are not included in the calculation of concentrations Normalized MFI Shows calculated normalization value No Fold Change Shows calculated fold change value No Sample Name User specified name for the well Yes Group Name The group number of the well Wells that Yes belong to the same group have the same group number Link Group Shows the control group number that is linked Yes to each well or well group MFI Average Shows the MFI average within the group No MFI Stdev Shows the MFI standard deviation within the No group O MFI CV Shows the MFI CV within the group N group within the group Average group within the group Intensity Shows the Normalized data within the group This data type is available in the lower drop down list only MasterPlex EX www miraibio com 21 CHAPTER3 GETTING STARTED Display Double Data Information in one Cell MasterPlex EX has an unique feature for data viewing on the well grid You can select two data type from various kind of data and it 1s displayed in the one cell separated into upper and lower Figure 3 8 shows how to display the double data in one cell MFI MFI ui Count MFI 20 00 5 3 lt Count 1084 50 82 00 88 Figure 3 8 Upper and lower grid display Well grid can be separated into upper and lower grid Each grid displays separate data type MasterPlex EX www miraibio com 22 CHAPTER3 G
87. utton S The Plate tab displays background subtracted data For more information on background calculation options see Background Type on section 4 6 Data type upper and lower drop down list Subtract Background button Display box Lower switch Sample Sample marking ico icon Command icon MFI naui g0 ET wg E Count 202 iS Sr Nr a a 1158 00 3 00 31 00 218 00 2 00 6 00 529 00 513 00 E Cla k A sceau asas casco RR hn m n nea E mi atia edi per s pl a LR moie D Re dean nee d noirs Lo Kien Mente p A Ere nne noe n Red I aint dec ng ea wh ACE cire n a e D Bee erra y ne 202 223 193 199 157 222 201 176 Be ICAM1 1280 00 4 00 36 00 248 50 2 00 7 00 553 00 600 00 F IFNG io Rae IN eect n sw peek rated D CC I ELLO Po oe en tO peers Ta ne CE Rate ee oo 227 186 209 168 199 207 229 233 AB MAPKS 289 50 2 00 7 00 57 00 2 00 3 00 485 50 340 50 Be Tcre1 E I 200 236 246 187 218 196 190 206 d TNF 284 50 2 00 11 00 66 00 2 00 3 00 607 50 377 00 232 201 182 172 719 194 224 152 54 00 543 00 3 00 18 00 151 00 3 00 340 00 3 00 Analyte Pane yt Well grid Figure 3 7 Plate tab and Analyte pane MasterPlex EX www miraibio com 19 Plate View Components Well Grid Data type upper and lower drop down list Lower grid switch Display box Analyte pane Sample marking icon Subtract background Command icon CHA PTER3 GETTING STARTED A representation of a microtiter plate
88. ve statement of the agreement between us which supersedes any proposal or prior agreement oral or written and any other communications between us in relation to the subject matter of this Agreement MasterPlex EX www miraibio com MuraiBio MasterPlex EX Analysis software for multiplex data from the Luminex 100 200 BioPlex system CONTENTS CHAPTER l PAGE Welcome About This Manual E 1 Technical Support P CHAPTER 2 Installing MasterPlex Requirements 3 Installing MasterBios s 4 Installing a License 10 CHAPTER 3 Getting Started Overview of MasterPlex EX Analysis 6 11 Starting MasterPlex EX ccccececeeeeseceeeceseeneseesesseees 12 Importing Luminex Results eese 13 Import csv xls Ixd or Open mlx mlx files by drag and drop T 15 Tab categorized work flow ee 16 Viewing Data in the Plate View 7770068 18 Saving Plate Data eeee 23 CHAPTER 4 Defining a Plate Plate tab Designating Well Type and Group crt 25 Setting Sample Amount 34 MasterPlex EX www miraibio com I Linking a Control DOUD erheen iii 40 Attach Housekeeping Gene Status 7668 4 Flagging the data Mee 42 Working With Templates V eskeseaosasotesssacnaesksqusauaa ee 45 Preferences MMMM eeeeeeAMM MMeQeQeeee
89. ve more than one housekeeping genes Link each well group to a control group to specify the control that 1s used to compute the analyte fold changes The plate definition can be saved as a template that can be applied to other plates The Template Manager helps you manage your templates For more information on templates see Working With Templates on section 4 5 4 1 Designating Well Type and Group Selecting Wells To select a well in the Plate tab click the well in the well grid There are three ways to select multiple wells To select adjacent wells Figure 4 1 press and hold the mouse button while you drag the pointer over the wells that you want to select Click and release the mouse button to select the highlighted wells To select adjacent wells press and hold the Shift key while you click the first and last well in the selection To select nonadjacent wells Figure 4 2 press and hold the Ctrl while you click the wells MasterPlex EX www miraibio com 25 CHA PTER4 DEFINING A PLATE 1 2 3 4 20 00 367 00 506 50 341 00 A ee ee ee rrmmr 63 67 76 80 1308 00 429 00 480 50 392 00 95 66 78 79 1084 50 82 00 88 00 78 00 72 79 75 70 525 00 88 50 82 00 96 50 D ee ee 7 79 66 76 74 201 00 37 50 38 00 37 00 E ee 81 82 85 96 66 50 32 00 32 00 34 00 NEN L LLL e 80 79 66 74 39 00 18 00 18 00 23 00 G uud ee ennnnnnnnnnnnn 78 81 68 68 Figure 4 1 Well grid To sele
90. x EX www miraibio com 110 APPENDIXA PREFERENCES Create Complex Filter Criteria To construct filter criteria involving multiple columns and various comparison operators use the filter drop down list and click Custom This invokes the Custom AutoFilter dialog Figure A 6 which allows you to compare a column with one or two values To construct using more various operators and multiple conditions use the filter builder See Basic step for constructing Filter Criteria by using Filter Builder paragraph in this section Custom AutoFitter Show rows where equals IL 10 And amp or equals Cancel Figure A 6 Custom AutoFilter dialog Filter Builder Window By using the filter builder you can filter the data more specifically To open the filter builder window choose Filter Editor from the right click menu on the column or click Edit Filter button on the bottom of the data grid Figure A 7 Well sample Mame sr ou Sort Ascending LN Sort Descending E d c Group By This Column 0 B Group By Box B gH Column Chooser H 4 Best Fit q WE Iv rics E Best Fit all columns Figure A 7 Opening the Filter Builder MasterPlex EX www miraibio com 111 APPENDIXA PREFERENCES Basic steps for constructing filter criteria with the Filter Builder 1 Right click on the grid column 2 Choose Filter Editor Filter Builder window appears Figure A 8 Click to change the current o
91. y groups replicates that follow similar group patterns 1 Define the group pattern by selecting a group of wells and marking and grouping them together We will group other wells into this pattern 2 Select all wells of the pattern group Figure 4 5 1306 00 429 00 480 50 392 00 95 66 J8 79 1084 50 82 00 58 00 78 00 masssasurazcs xssmcmm mmm mmm mmm eee Rm men 7 79 75 70 525 00 88 50 82 00 96 50 D ee es ee ee 79 66 7O 74 201 00 of 38 00 37 00 81 82 85 96 66 50 32 00 32 00 34 00 8l 79 55 74 39 00 18 00 18 00 23 00 G see ee ee F8 81 58 69 25 50 19 00 17 50 27 00 68 69 80 42 Figure 4 5 Well groups MasterPlex EX www miraibio com 29 CHA PTER4 DEFINING A PLATE 3 Move the pointer to the bottom right corner of the selection When you see the pointer turn into a black cross hold down the left mouse button and drag the pointer over the selection During dragging you will see in real time that new wells are selected and grouped into the pattern as indicated by a red line border Figure 4 6 2 3 4 367 00 506 50 341 00 A ee SAT eee ee eee eer eee eee ee 57 76 80 420 00 480 50 392 00 B ao Lunanamnummuumuauuuninmunuuumuuuunumum iumumuuuuuumuREM 66 78 79 82 00 cp ae T A C DS S een al 57 76 80 88 50 ES 55 66 EB eee 201 00 37 50 E ht annaa IE 81 82 66 50 32 00 F rre rope mcam nee 80 79 D 39 00 18 00 EM 7m ail E 26 50 19 00 s 68 69 t F G 26

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MasterPlex® - Hitachi Solutions America