[BioC] [DESeq] p-value vs adjusted p-value

[Simon Anders]

On 05/06/13 17:06, lucia kwak wrote:
> Hi all,
>
> Thank you for your answer. I've used method=blind to estimate the
> dispersions in DESeq. For the comparison of tools, I am using different
> p-value cutoff for two packages making the similar subset size of
> significant genes. The adjusted p-value in edgeR is much lower than the
> p-value used in DESeq.  But if I use the adjusted p-value in DESeq also, it
> is hard to find the differentially expressed genes, while the edgeR shows
> many significant genes.

I am getting confused here. I sounds as if at some point you are 
comparing raw p values from one tool with adjusted p value from the 
other tool. This would make no sense at all.

Also, you used the "blind" dispersion estimation mode in DESeq. Have you 
used the equivalent option for edgeR? (Sorry, I forgot how the edgeR 
people call their variant of a blind estimation but they have something 
similar.) I do remember that edgeR can somehow be switched to a "Poisson 
mode" in case of no replicates, where the dispersion is set to zero. 
Long ago, this was the default, but this is (reasonably) no longer the 
case, I think.

Maybe post the code you used.

   Simon