I need greater accuracy in the FDR value than that afforded by the default number of 5 randomizations. Can I compute the FDR value using more randomizations than the default number?
The number of randomizations can be increased by first selecting a desired root category for the FDR computation as described in the previous question. Select a category, then right click, and choose ‘More Robust FDR.’ from the pop-up menu A dialogue box will appear that allows you to select a larger number of randomizations. This will recalculate the FDR’s from that node down to the bottom of the ontology. Categories that are not in the selected path will have their FDR’s cleared when you recalculate. Because the computation may take a few minutes, we present a progress bar so that you will know when it is completed. You can interact with the system while the FDR’s are recalculated, but the FDR values aren’t stable until the process is complete.
