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To get a sense of what filtering thresholds to set, we can view a volcano plot for a comparison. 

• Select Click  next to the 5uM vs. 0uM comparison 

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Thresholds for the cutoff lines are set using the text boxes on the left-hand side. The default thresholds are 2 and 0.05. 

• Select Gene-specific analysis Click GSA report to return to the task report spreadsheet
• Select Click FDR step up
• Select Click the triangle next to FDR step up to open the FDR step up options
• Select Leave All contrasts selected
• Set the cutoff value to 0.05

This will include genes that have a FDR step up value of less than or equal to 0.05 for all three contrasts, 5μM vs. 0μM, 10μM vs. 0μM and 5μM:10μM vs. 0μM. FDR step up is the false discovery rate adjusted p-value used by convention in microarray and next generation sequencing data sets in place of unadjusted p-value. 

• Select Click Fold-change
• Select Click the triangle next to Fold-change to open the Fold-change options
• Leave All contrasts selected
• Set to From -2 to 2 with Exclude range selected

Note that the number of genes that pass the filter is listed at the top of the filter menu next to Results: and will update to reflect any changes to the filter. Here, 21 29 genes pass the filter (Figure 3).

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• Select Click  to create a data node with only the genes that pass the filter

This creates a Filtered gene analysis Filter list task node and a Feature list data node (Figure 4).

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