[BioC] Separating gene filtering and multiple testing p-value adjustment steps

[FeiYian Yoon [guest]]

Hi, 

In DESeq2, gene filtering and p-value adjustment for multiple testing are done under the same result function. I'd like to perform these two steps separately. To illustrate, I'd like to perform gene filtering for all my genes for all samples. But, for the multiple testing for differential expression, I'd like to do it with only a subset of samples for my comparisons of interest. How do I separate these two steps?

Also, I'd like to normalize my samples with endogenous genes that are stably expressed. Do I do it before p-value adjustment for multiple testing (differential expression)?

Thank you in advance!

Yoong

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