Sort rows Rows by prototype Prototype is a function that can identify genes with similar expression patterns. For example, if a gene with an interesting expression pattern has been detected, using Sort Rows by prototype Prototype makes it possible to find other genes that have a similar pattern of intensity values. Although this is most commonly used for changes in gene expression over a time course, it can be applied to other experimental designs as well.

To invoke Sort rows Rows by prototypePrototype, probe(sets)/genes must be on rows. If you want to use this tool to analyze the main intensity values spreadsheet, the spreadsheet must be transposed prior to analysis. A common way to view and analyze gene expression in a time-series experiment is to include means or LS means in the ANOVA spreadsheet.

• Configure the ANOVA dialog to include the factor or interaction of interest
• Select Advanced... from the ANOVA dialog
• Select LS-Mean or Mean 
• Use the drop down menus to select the factors or interaction you want the LS mean / mean of
• Select Add for each
• Select OK (Figure 1) 
  
  

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• Select OK to close the ANOVA configuration dialog and open the ANOVA spreadsheet

The Sort rows Rows by prototype Prototype function uses every non-text column in a spreadsheet to build and compare patterns; any columns you do not want to include in the pattern similarity analysis need to be removed before running the function. 

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• Select columns you want to remove
• Right-click on a selected column headers
• Select Delete from the pop-up menu
• Select () from the main command bar to save the modified spreadsheet

We can now invoke Sort rows Rows by prototype Prototype on the modified spreadsheet.

• Select Tools from the main toolbar
• Select Discovery
• Select Sort Rows by Prototype... (Figure 2)
  

The Sort Rows by Prototype dialog will launch (Figure 3). 

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This dialog allows you to configure the pattern, or prototype, that all probe(sets)/genes will be compared to by Sort Rows by Prototype. 

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• Select the row headers of the top 5 rows by selecting each while holding the Ctrl key or selecting the first and then fifth while holding the Shift key
• Select View from the main toolbar
• Select Profiles
• Select Row Profiles 
  
• Select Select for both Plots and X-Axis in the Configure Data Source dialog

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