Re-calculation of Padj (P adjusted value)
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Matan G. ▴ 40
@matan-g-22483
Last seen 4 weeks ago

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

statistics Benjamini–Hochberg procedure deseq2 • 200 views
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@mikelove
Last seen 5 hours ago
United States

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.

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Hi Micahel,

Thank you for answering.

All the best

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