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The task report spreadsheet will open showing genes on rows and the results of the GSA on columns (Figure 1).
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To get a sense of what filtering thresholds to set, we can view a volcano plot for a comparison.
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A volcano plot will open showing p-value on the y-axis and fold-change on the x-axis (Figure 2).
If the gene labels are on (not shown), click on the plot to turn them off.
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Thresholds for the cutoff lines are set using the text boxes on the left-hand side Significance card (Configuration panel > Content > Significance). The default thresholds are 2 are |2| for the X axis and 0.05 for the Y axis.
- Click GSA report Switch to return to the task report spreadsheetthe browser tab showing the GSA report
- Click FDR step up
- Click the triangle next to FDR step up to open the FDR step up options
- Leave All contrasts selected
- Set the cutoff value to 0.05. Hit Enter.
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.
- Click Fold-change
- 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. Hit Enter.
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, 29 32 genes pass the filter (Figure 3).
Depending on your settings, the number may be slightly different.
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- Click to create a data node with only the genes that pass the filter
This creates a Filter list task node and a Feature a Filtered feature list data node (Figure 4).
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