Hi,

The output of DESeq2 gives P values and Padj (Padjusted value). I am trying to understand if it is appropriate to apply a post filtration (i.e. after analysis) according to max counts (i.e. setting a threshold for the raw counts post filtration) and use the p values to re-calculate the adjusted P values accordingly.

Best,

Matan

DESeq2 already filters on the mean normalized count over all samples, and this has been well tested. I don't think that max count will be a better filter than the mean.

If you want to explore optimal filtering by count level per gene, see the IHW section of the vignette.