independent filtering on the gene counts

[shivarice]

Is there a way for someone to perform an independent filtering on the count data instead of using the meanCountTestableThreshold variable?

[hartleys]

I would recommend just turning the independent filtering off (set meanCountTestableThreshold = -1), then you can do the test filtering after the fact. Just filter the output table by whatever stats you want, then recalculate the adjusted p-values using the "p.adjust" function.