Remove low-expressed genes in DESeq2?
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erbrocato • 0
@dfeb9251
Last seen 6 weeks ago
United States

Hi,

I have run my initial analysis without filtering for low-expressing genes, given DESeq2's independent filtering procedure. Due to the low number of significant genes returned when using an FDR, we have opted to use an unadjusted p-value cutoff so that we can generate a gene list of sufficient length for GO analysis. Because DESeq2's independent filtering informs the FDR adjustment, is it recommended that I remove low-expressing genes prior to running DESeq2 if I'm using an unadjusted p-value? Or is the independent filtering threshold considered when using an unadjusted p-value cutoff as well? I am using DESeq2 v1.32.0.

Thanks for your help, Emily

DESeq2 lowcountgenes deseq2 independent • 353 views
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It is not clear to me that anyone will recommend you use unadjusted p-values under any circumstances. If your treatment or whatever really doesn't change many genes, playing games with the math is not going to make the experiment better.

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