Step 3 - Select comparisons

The third step of the Create a Quick Gene Set wizard appears below.

In this step, check one or more threshold values to determine inclusion in the set.

•      To compare all genes against a signal threshold to determine if they should be included in the results, check the box next to Signal Threshold and enter a value in the box at right. When comparing pairs, the higher of the two experiments must exceed this threshold. If you used DESeq2 or edgeR normalization, Signal Threshold uses the linear rlog values calculated by that method.

•      To compare the fold change for each gene in a pair of experiments to determine if the gene should be included in the results, check the box next to Fold change. This option is only available if you chose pairwise or baseline comparison in Step 1.

Edit the Fold change threshold, if desired, using the arrows or by typing a number into the text box. Check the boxes next to Up and/or Down to specify the direction of the fold change you want to use for creating sets.

If you used DESeq2 or edgeR normalization, the Fold change uses linear values of the log₂ fold change calculated by that method.

•      To use a maximum P-value threshold to determine if a gene should be included in the results, check P-value. This option is only available for replicate sets, and only if you chose pairwise or baseline comparison in Step 1.

o  Enter a value in the box at right. An item (e.g., gene, isoform, etc.) will only be included in a set if the P-value for the expression signal in the given comparison is greater than the threshold specified here.

o  Use the Statistical Test dropdown menu to choose whether to calculate the P-value using the Student’s t-test or Moderated t-test.

o  Use the Correction Method dropdown menu to choose the multiple testing correction to be used in the t-test calculation.

If you used DESeq2 or edgeR normalization, the P value uses the adjusted P value calculated by those methods.

To return to an earlier step, click its “up arrow” button ().

If you are satisfied with the criteria in the three wizard steps and wish to generate quick sets, click Finish. These sets will then be available in the Set List.