How does LeFE compute an FDR?
Running LeFE requires a lot of computing power, as is evident by the long processing times. Therefore, we have developed a fast running version of LeFE that preliminarily runs all gene categories through the algorithm quickly and then refines the statistics on the highest scoring (lowest p-value) categories. This faster version allows for us to run 4 FDR iterations and we find that that method provides suitably stable FDR estimates.
