Visualization
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1. is the top level spreadsheet e Select the categorical factor like dose or time for the X axis Even though the variable is categorical PGS will recognize the values as numbers if there are no units in the column use 8 15 10 and not 8h or 15ug e Select the categorical factor of choice like treatment for Separate by This category will be used to color the response lines or symbols e Select the appropriate probe set for Y axis e Optionally choose a Line Style e Select OK Visualizations of Microarray Data in Partek Genomics Suite 6 6 8 a Time 2 Treatment 6 100 9 at O Mean LS Mean igure 10 XY Plot dialog A customized XY plot is shown in Figure 11 XV Barchart Plot c1 v1 oa ol eS File Edit View Window Help ke BOB Color 7 Auto OrigOrder K PI E P R a DYRK4 a 6 93 6 889 6 849 6 808 6 767 6 727 LS Mean 6 686 6 645 6 605 6 564 x Control E2 E2 ICl e E2 Ral s E2 TOT 6 524 0 S 48 Time Figure 11 Customized XY Plot Only the control was measured at time 0 DYRK4 expression goes up from time 8 to 48 hours for some treatments but for other treatments its expression decreases This indicates the need to include an interaction term Treatment Time in the ANOVA model Visualizations of Microarray Data in Partek Genomics Suite 6 6 9 Visualize P values and Fold Change Volcano Plot The volcano plot is used to visualize p values and fold changes2. the gene symbol and the columns containing means of each time point Clone the spreadsheet before deleting columns from the ANOVA spreadsheet Then an expression profile can be drawn by one of the options discussed in this user guide For instance a differentially expressed gene was picked because its expression signature is relevant for the study the expression goes up from the first to the second time point and then remains unchanged Figure 19 Profile c1 v1 File Edit View Window Help e k a OGCoks 21SMean Co v Selected Rows Q 11 05 10 8 10 56 10 32 10 08 g 9 84 96 9 36 912 8 88 8 64 LSMean Control 0 LSMean E2 8 LSMean E2 48 SS s Column a ea ee ee ee Figure 19 An example of expression signature in a time series study including three time points Visualizations of Microarray Data in Partek Genomics Suite 6 6 15 To find the genes with similar expression signature select Tools gt Discover gt Sort Rows by Prototype In the Sort Rows by Prototype dialog select From Row to indicate that the prototype is one of the genes in the spreadsheet and then choose the appropriate spreadsheet row by using Use this row as prototype Alternatively you may drag the points in the plot to create a shape of interest or use any of the predefined Pattern types by selecting the appropriate shape icons The display will automatically be changed to show the profile of the sel
3. Label Format section of the dialog select the pull down next to Column and choose the label you would like displayed If the label you have selected is long you may also want to select Rotate axis labels The labels will be rotated in a counter clockwise direction e If you wish to change the labels on the plot select Titles e Use the Styles tab to vary the line thickness to add symbols to the lines e To add your own text strings to the graph use the Text tab e Select OK or Apply Visualizations of Microarray Data in Partek Genomics Suite 6 6 5 Aut i Plot Properties c1 v1 Style Labels Bow amp iWVhiskers Legend C Invert X and Y axes Axis Font Size 14 Configure Axes Axis X Placement bottom Show Axis Labels Grid Major 10 2 Mnor 2 4 C Rotate X Axis Labels 90 degrees Label Format Row Row Name Column 1 Filename Figure 7 Plot properties dialog Visualizing Dot and Profile Plots for Some Samples The dot and profile plots in the previous section display the intensity profiles across all of the samples in the parent spreadsheet indicated by the Orig Data in the plot commands If you wish to exclude certain groups of samples from these plots then filter those rows from the parent spreadsheet before generating the plots Visualize Gene Intensity Values across Groups Group Profile Plot If you wish to generate a profile plot across levels of a factor then the Group Profil
4. View Window Help Grovpby 2 Treatment hd HV MOM Color 2 Treatmet d e D gt ry a ATP binding cassette sub family C CFTR MRP member 5 9 0 O 8 78 O O 8 56 CO 8 34 O e Control O E2 8 12 9 O O g 78 O x O 7 68 7 46 O 7 24 7 02 CO 6 8 Control E2 E2 ICIE2 Ral E2 TOT Figure 3 Simple dot plot of a single gene that shows the distribution of probe set gene intensities across all samples The dot plot shown in Figure 3 is perhaps the simplest version of the plot that can r be generated Using either Edit gt Plot Properties or the in top left of the menu many other customizations may be performed E pS File Edit View Window Help te a Group by 2 Treatment HV BOMS Color 2 Treatment lt q PID E ATP binding cassette sub family C CFT R MRP member 5 o H H g E CE 6 8 Control 3 E2 IC E Ral E2 TOT igure 4 Dot plot visualized by editing plot properties and changing options in the Box amp Whiskers tab Visualizations of Microarray Data in Partek Genomics Suite 6 6 3 The default order of the groups in the Dot Plot is alphabetical order To change the order to match what is specified in the parent spreadsheet then use either Edit gt Configure Plot or the icon and select Categoricals in spreadsheet order Visualize Intensity Values across Samples Profile Plot In contrast to the dot plot which shows one probe set gene pe
5. Visualizations of Microarray Data in Partek Genomics Suite 6 6 This tutorial will illustrate how to e Visualize intensity values across samples via a dot plot Visualize intensity values across samples in a plot Visualize intensity values across levels of a categorical factor Visualize intensity value of one probe time series Visualize fold change and p values in a volcano plot and choose genes with particular significance levels e Visualize gene expression patterns across two samples Scatter Plot and MA Plot e Find other genes with similar a similar intensity profile across all samples e Create a Manhattan plot showing the log p value vs the genomic location This tutorial assumes the user is familiar with the hierarchy of spreadsheets and analysis in Partek Genomics Suite PGS More details about customizing plots can be found in Chapter 6 of the Partek On line Documentation available from Help gt User s Manual from the main toolbar The data for visualizations in PGS comes from a spreadsheet If you only wish to include certain rows or columns in a plot you may need to apply a filter and or clone the spreadsheet or select only certain rows or columns There is no specific dataset for this tutorial you may use one of your own microarray experiments or use the data from another tutorial In general gene intensity values may be visualized from either an ANOVA spreadsheet or a filtered ANOVA spreadsheet Since the
6. ased on their similarity to the prototype gene Smaller proximity values imply more similarity to the selected shape You can generate a profile plot of several of the rows for instance the top five most similar e Select the row headers of the top 5 rows shift select or ctrl select e On the top menu select View gt Profiles gt Row Column Profiles e Specify rows for Curves on e Next to Curves select Selection as List as shown in Figure 22 Create Row Column Profiles 2s Configure Data Source Curves on rows r Curves list Selection As List 12345 X Axis all Selection As List Color gO Width gee Fixed Hi Line Width Selected Width Symbol Size 1 Proximity to prototyp 7 Auto Plot Style ines Symbol None Qutine Thin Figure 22 Generating a profile plot of the five probe set s most resembling the specified shape by Sort rows by prototype Visualizations of Microarray Data in Partek Genomics Suite 6 6 17 Gomi he i See es File Edit View Window Help te BOH Coler 1 Proximity to Rows 12345 2 Value 6 62 6 03 5 43 484 424 Brain 01 vi_WTGeneTiCELpimg TisMap_ TisMap _ TisMap _ TisMap _ Column A Figure 23 Profile plot of 4 probe set s plus the original prototype most similar to the prototype used in Sort rows by prototype Visualize Genomic Coordinates and P values Manhattan Plot A Manhattan plot is a common way to vis
7. ce with these steps you may call our technical support staff at 1 314 878 2329 or email support partek com Last revision April 2 2012 Copyright 2012 by Partek Incorporated All Rights Reserved Reproduction of this material without express written consent from Partek Incorporated is strictly prohibited Visualizations of Microarray Data in Partek Genomics Suite 6 6 20
8. e plot option is used Group Profile plots are generated from the parent spreadsheet by selecting the columns that correspond to the probe set s you wish to display The first step is to select the columns from the top level parent spreadsheet This can be done in a couple of different ways e You may control left click on the columns corresponding to the probe set s you wish to display Be sure to also select the column that contains the categorical factor which should be used for grouping the intensity values OR e From a spreadsheet where probe set s are found on rows like ANOVA or a filtered ANOVA spreadsheet select the rows which should be displayed Then right click on one of the selected row headers and choose Select Orig Data Then open the top level or Visualizations of Microarray Data in Partek Genomics Suite 6 6 6 parent spreadsheet and Ctrl left click on the column with the categorical factor to be used in grouping e From the command toolbar select View gt Profiles gt Group Profile which brings up the Create Group Profile dialog shown in Figure 8 Notice that the columns which were selected by either of the methods described above are shown next to Selection as List These numbers are the column numbers of the probe set s Spreadsheet Curve Set new Group by 2 Treatment Columns list Selection As List 4775 28519 14895 8334 X Axis Columns Groups Y Axis Mean Median Figure 8 Create Grou
9. ected gene Please note that the scale of the y axis of the original profile plot and the Sort rows by Prototype plot are different compare Figure 19 and Figure 19 but the data is the same Sort Rows by Prototype of Spreadsheet 1 profile leme oe Syl Generate Pattern Pattern Type N IZIR ANCA From Row Use this row as prototype Select Dissimilarity Measure Euclidean hd Manually Configure Prototype By Dragging Points cres Figure 20 Sort Rows by Prototype dialog Choose one of the dissimilarity measures some are parametric and some are non parametric Select Sort to proceed The resulting spreadsheet will have the genes reordered Figure 21 so that the prototype is in the first row while the other genes are listed based on their similarity to the prototype gene as expressed by the Proximity to prototype column Visualizations of Microarray Data in Partek Genomics Suite 6 6 16 _ Current Selection 2 76973e 007 i 2 8 64204 10 988 11 045 CA12 8 64991 10 2622 10 6686 MYOF 8 99804 10 3305 10 6016 IGFBP4 9 44883 11 0448 11 3988 SLC7A5 8 88598 10 2744 10 557 JAK1 9 33914 10 2201 10 4327 TFRC 9 88317 10 737 10 9602 ZNF 146 9 19471 10 2631 10 1589 RAB31 8 05606 10 0761 10 3553 MTHFD2 9 50359 10 2918 10 3822 DKC1 9 7922 10 4222 10 8626 FEN1 9 40547 10 2743 10 2726 Figure 21 Result of sorting by prototype The prototype gene is in the first row while the other genes are listed b
10. etween the two samples for the same data point In essence an MA plot is a scatter plot tilted to the side so that the differentially expressed genes or probe sets are located above or below the 0 value of M An MA plot is also useful to visualize the results of normalization where you would hope to see the median of the values follow a horizontal line Unlike the scatter plot the MA plot is invoked on the original intensities spreadsheet View gt MA Plot The two samples for comparison are then directly selected in the lists on the left Figure 17 Visualizations of Microarray Data in Partek Genomics Suite 6 6 13 B CP MA Plot Spreadsheet 1 File Window Q Select Sample 1 Down Syndrome Cerebru Down Syndrome Cerebru Down Syndrome Heart 1 Down Syndrome Heart 1 4 00 MA Plot Down Syndrome Astrocyte 748 1 U133A CEL Normal Astrocyte 1479 1 U133A CEL Normal Astrocyte 1479 1 Normal Astrocyte 1521 1 Normal Cerebellum 1390 Normal Cerebellum 1411 Normal Cerebellum 1521 Normal Cerebrum 1390 1 Normal Cerebrum 1390 2 _ 2 24 Normal Cerebrum 1411 1 gt Normal Cerebrum 1411 2 Normal Cerebrum 1521 1 Normal Cerebrum 1521 2 Normal Cerebrum 1565 1 Normal Heart 1390 1 U1 Normal Heart 1411 1 U1 0 48 Difference Select Sample 2 own Syndrome Astrocy own Syndrome Astrocy own Syndrome Cerebell own Syndrome Cerebell own Syndrome Cerebell 1 28 own Syndrome Cerebru own Syndrome Cerebrul _ o
11. he plot Edit gt Plot Properties Once in the Axes tab select Set Regression Lines In the Set Regression Lines dialog Figure 15 select Regression line of y on x box and increase the Line Width e g to 5 points A formatted plot is shown on Figure 16 Use the Selection Mode of the plot to pick the data points of interest Right click on the plot and select Create List to dump the list of genomic features to a spreadsheet note column with gene ID or probe set ID needs to be selected first ty Set Regression Lines spl as W Regression line of y on x Color Hi Line Width 5 E 95 Confidence Interval lines Color Hl Line Width 1 E Label None Slope Linear Correlation Gai Figure 15 Set Regression Lines dialog Visualizations of Microarray Data in Partek Genomics Suite 6 6 12 yy Scatter Plot sp1 v1 o E liom File Edit View Window Help K e MOM Colr 2 Down Syndrome 20180 rk a Scatterplot of 2 fa P Regression Line ta r 0 972356 gs Bee e be 2 4 Normal 2 3 2 44 5 6 6 8 8 9 2 10 4 11 6 12 8 14 Down Syndrome Thala W eal Mai Figure 16 Customized scatter plot Each dot on the plot represents the expression value of a genomic feature gene or probe set Alternatively the MA plot can be used to display a difference in expression patterns The horizontal axis A shows the average intensity while the vertical axis M shows the intensity ratio b
12. intensity data is stored in the parent spreadsheet both spreadsheets should be visible in the spreadsheet navigator with the appropriate parent child relationship Figure 1 E 1 Breast_Cancer txt 1 ANOVAResults 2 E2 vs Control Figure 1 Breast Cancer is the parent spreadsheet both ANOVAResults and E2 vs Control are children of Breast_Cancer txt Visualizations of Microarray Data in Partek Genomics Suite 6 6 1 Visualize Intensity Values across Samples Dot Plot The primary use of the Dot Plot is to visualize the distribution of the gene intensity values of one gene across all samples e Select the row s in the spreadsheet containing the gene s to be visualized by right clicking on the row header e Right click and select Dot Plots Orig Data The Orig Data is an indicator that the gene intensity values will be taken from the original data contained in the parent spreadsheet Figure 2 Copy Paste Filter Indude Filter Exdude Select Orig Data Insert Delete HTML Report Dot Plots Orig Data Profile Orig Data Transcript HTML Report Create List 4 Figure 2 Creating a dot plot of gene intensity values A dot plot will be displayed in another window Figure 3 If multiple probesets are selected then multiple dot plots will be generated in separate windows Visualizations of Microarray Data in Partek Genomics Suite 6 6 2 Dot Plot sp8 v8 File Edit
13. llele v Fixed E Error Bars fe Off f Standard Error Split profile on none value 0 Location Inside chromosome Outside chromosome V Overlap Profiles Smoothing C Auto Manual 1 4 Draw profile on all selected InPointLabel Precision 2 Label Samples 5 Low Frequency 7 Axis Min Max by Genome Chromosome Values 0 0 V Show Label V Show Grid 6 Logscale Base 2 Style ame Shape Size m point v Connect Points 0 5 Figure 24 Configure Profile dialog An example of the Manhattan plot is shown on Figure 25 By selecting chromosomes in the upper left corner it is possible to focus on particular regions of genome Please note that the lining of the dots in Figure 25 1s an artifact caused by the small number of samples and will not be apparent in a large study Visualizations of Microarray Data in Partek Genomics Suite 6 6 19 r G ChrView cv1 v1 2 E amp File Edit View Window Help hA Clear Selected Zoom in Zoom out 1 564621 249198692 Cytoband Ha 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 MT X Y Show All Clear All X chisq p value allele 3 g Ain a Figure 25 Customized Genome Dot Plot showing genomic location on the x axis and log1o P value of a SNP on the y axis Manhattan plot Each dot represents a single SNP End of Tutorial This is the end of the tutorial If you need additional assistan
14. nes but all the genes in a region delimited by cut off lines Although p value was used to color the plot the horizontal cut off value will not match the default coloring scheme 1 e some non significant genes will be colored by a shade indistinguishable from the ones used for significant genes e Select Edit gt Plot Properties and select the Color tab e Inthe Mid box of Color scaling section type 0 05 Visualizations of Microarray Data in Partek Genomics Suite 6 6 10 CF Set Cutoff Lines sp1 gt S Vertical Line s X Axis Value s 2 Horizontal Line s Y Axis Valuefs 0 05 E Select all points in a section Line Color Line width 3 Figure 13 Setting the cutoff lines in the volcano plot The genes or probe sets of interest are now in the upper right and upper left sections of the plot If you have used the Select all points in a section option during the plot formatting see above then left clicking on a section will select all the genes in the section However if the Select all points in a section option was not used it is possible to use the Selection Mode of the plot to manually select genes of interest An example is shown in Figure 14 probe set IDs of the selected sets are highlighted F Sr eS a a J Volcano Plot sp1 v1 File Edit View Window Help BOM Color 7 p value Astrocyte and Cerebell 2D 3D Volcano Plot of 1 1 p value Astrocyte and Cerebellum an Fig
15. of genomic features e g genes or probe sets at the same time and allows for quick identification of differentially expressed genes with a certain level of expression Please note that the same list generation can be achieved by List Manager ANOVA Streamlined tab To invoke the volcano plot please follow these steps e From the View menu select the Volcano Plot e The Volcano Plot Configure dialog Figure 12 will instruct you to specify a fold change column x axis and a matching p value column y axis The choice of Color by option is arbitrary but choosing the same p value enables for quick identification of differentially expressed genes tf Volcano Plot Configure 1 1 x Axis Fold Change 9 Fold Change Astrocyte and Cerebellum and Cerebrum vs Heart Y Axis p value 7 p value Astrocyte and Cerebellum and Cerebrum vs Heart Color by 7 pevalue Astrocyte and Cerebellum and Cerebrum vs Heart Cancel Apply Figure 12 Volcano Plot Configure dialog Once the plot is generated the key regions of the plot can be highlighted by setting the cut off lines e Go to Edit and select Plot Properties e Inthe Axis tab select the Set Cutoff Lines Figure 13 e The Vertical Line s refer to the cut off values of the fold change for instance 2 or 2 while the Horizontal Line refers to the cut off value for the p value e Ifyou select the Select all points in a section box then a left mouse click will not select single ge
16. p Profile dialog e Select the proper column for grouping in the Group by pull down menu e Select Groups for the X axis option e Select either Mean or Median in the Y Axis option e Select OK The basic Group Profile plot is shown in Figure 9 It is likely that you would like to customize the plot using the options shown in the Plot Properties dialog depicted in Figure 7 One customization specific to this plot would be to display the standard deviation or error bars Customize the plot and use the Error Bars tab to add either standard error bars or standard deviation bars Visualizations of Microarray Data in Partek Genomics Suite 6 6 7 F Profile c1 v1 a File Edit View Window Help te Group by 2 Treatment hd BOA Color Auto k a Group Profile of Treatment A 8 93 8 15 7 37 6 6 5 82 o 3 S 5 04 Oo se 4 26 3 49 2 71 1 93 1 15 Control 2 2 CI E2 Ral E2 TOT Treatment Figure 9 Group Profile plot across levels of one categorical factor Treatment Visualize Intensity of One Probe Set Across Two Factors Time Series The XY plot can be used to display the effect of two categorical variables like time and treatment or dose and treatment on a response variable Only one probeset may be visualized at a time e From the top level toolbar select View gt XY Plot Barchart which invokes the dialog shown in Figure 10 e The Spreadsheet that is selected must contain the categorical variables that
17. r plot the profile plot is used to visualize how the intensity values from multiple genes compare across all samples e From the spreadsheet where probe set s genes are located on rows select the rows which should be displayed on the profile plot e Right click on one of the rows and select Profile Orig Data as shown in Figure 5 Copy Paste Filter Indude Filter Exclude Select Orig Data Insert Delete HTML Report Dot Plots Orig Data Profile Orig Data Probe Set Details Probe Set HTML Report Create List Figure 5 Generating a profile plot Visualizations of Microarray Data in Partek Genomics Suite 6 6 4 File Edit View Window Help K Value BOG Color Column Traces 9 4 hp fl fob for fase ape wn EDES ESS DES ISi EE ERE cet mt LAT eft OL SERA NS SSS SAA e EEHEEHE NEHHA HR at H EEEN EE PRE NGI eb tee ee Row 1 Row 2 Row 3 Row 4 Row 5 Row 6 Row 7 Row 8 Row 9Row 10Row 11Row 122ow 13Row 14Row 15Row 16Row 1 7Row 18 33799 atm 32668_at 40674_s_at 38312_at Row Figure 6 Basic profile plot Each line represents a different probeset gene each column represents a sample from the parent spreadsheet e The basic profile plot shown in Figure 6 will likely need customization To change the labels in the x axis from Row to the sample name or categorical variable select either Edit gt Plot Properties or this brings up the dialog shown in Figure 7 e Select the Axes tab In the
18. sheet the defaults are acceptable so select OK The column order in the transposed spreadsheet will be used for the graphs If the columns need to be reordered then select the column header and drag it to the border adjacent to its new location When you see the cursor change to a hand with an index finger you may drop the column in its new location One of the ways to depict gene expression in a time series experiment is to include means or Ismeans in the ANOVA spreadsheet That option can be set by selecting Advanced in the main ANOVA dialog and adding the groups to be summarized in the ANOVA spreadsheet An example is shown in Figure 18 Visualizations of Microarray Data in Partek Genomics Suite 6 6 14 Yv Click Add button to add items to the display panel Obs M LSMean M Mean Std Dev Std Err Min Max 2 Treatment 4 Time Value vy alllevels Factor Interact 2 Treatment 4 Time 2 Treatment 4 Time 2 Treatment 4 Time 2 Treatment 4 Time 2 Treatment 4 Time 2 Treatment 4 Time 2 Treatment 4 Time 2 Treatment 4 Time Level Control 0 E2 48 E2 8 E2 ICI 48 E2 ICI 8 E2 Ral 48 E2 Ral 8 E2 TOT 48 2 Treatment 4 Time E2 TOT 8 Figure 18 Using Advanced ANOVA setup to include group means in the ANOVA output To get a plot of expression levels across the time points some changes need to be made to the ANOVA spreadsheet all the columns need to be removed except
19. ualize the results of GWAS study with genomic coordinates on the x axis and log o P value of each SNP on the y axis Therefore the starting point for a Manhattan plot is a spreadsheet with SNPs on rows and P values in a column To begin it is needed to take the logio of the P values e Select the column with the P values and go to Transform gt Normalization amp Scaling gt On Columns e Inthe Normalization tab set the Base of the Log x offset to 10 and select OK e Goto Transform gt Normalization amp Scaling gt On Columns again Choose the Add Mul Sub Div tab and set the Multiply by Constant to 1 and press OK Visualizations of Microarray Data in Partek Genomics Suite 6 6 18 e Invoke the initial plot by View gt Genome Dot Plot To proceed go to Edit gt Plot Properties and select the Dot Plot tab Uncheck the Show Dot Plot box and select Apply the plot will become blank e Proceed to the Profiles tab and select Add Profile The Configure Profile dialog will appear Figure 24 The Column should point to the spreadsheet column containing the P values In addition set the Smoothing to Manual set the Style to point and decrease the Shape Size to 0 5 Select to OK to accept these settings and then OK to show the plot a Configure Profile Configure Profile Spreadsheet 4 ChiSquare_col2_1 ptmp11 v Mean Column Separate by sample Color by Value Category Column 2 chisq a
20. ure 14 Customized Volcano Plot Each dot represents one probe set Cut off lines show critical p value horizontal line and critical fold change vertical lines The dots are colored by p value with all the significant probe sets having blue color By using Selection Mode two probe sets in the upper left were selected Moreover if you want to generate a list of selected genes right click on the probe set labels in the plot and go to Create List Please make sure that the Gene Symbol Visualizations of Microarray Data in Partek Genomics Suite 6 6 11 column of the ANOVA spreadsheet is selected before you actually perform the creation Visualize Differentially Expressed Genes Scatter plot and MA plot A simple and common way to visualize the microarray data 1s the scatter plot showing the comparison of gene expression values for two samples at one time While most data points 1 e genes or probe sets fall on a 45 line up or down regulated genes are positioned above or below the line To draw a scatter plot you first need to transpose the original intensities spreadsheet so that the samples are on columns and genomic features genes or probesets are on rows Transform gt Create Transformed Spreadsheet Once the spreadsheet is transposed proceed as follows Select the two columns containing the samples you would like to compare Go to View gt Scatter Plot to display the plot A regression line can be displayed by editing t
21. wn Syndrome Cerebrul Down Syndrome Cerebru Down Syndrome Heart 1 Down Syndrome Heart 1 3 04 INormal Astrocyte 1521 1 iNormal Cerebellum 1390 jormal Cerebellum 1411 lormal Cerebellum 1521 i j l 1 jormal Cerebrum 1390 1 3 8 6 2 8 5 10 9 13 2 jormal Cerebrum 1390 2 Average Figure 17 MA plot comparing the expression levels between two samples Each dot on the plot represents a single genomic feature gene or probe set The average signal for each genomic feature is shown on the horizontal axis A while the ratio is shown on the vertical axis M Visualize Identify Genes with Similar Expression Patterns PGS s function Sort rows by prototype enables you to identify genes with similar expression profiles For instance if a gene with an interesting expression pattern has been detected using Sort by prototype makes it possible to find other genes that have a similar pattern of intensity values Although this functionality is commonly used for time series experiments 1t can also be successfully applied to other experimental designs as well As the name of the function Sort rows by prototype implies intensity values must be on rows and values on columns when using this feature The top level spreadsheet contains the intensity values for all probe set s but must be transposed before this function is used Select the top level spreadsheet and use Transform gt Create Transposed Spread
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