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

Davide Cittaro cittaro.davide at hsr.it
Wed Jun 5 16:42:40 CEST 2013

On Jun 5, 2013, at 4:25 PM, Steve Lianoglou <lianoglou.steve at gene.com> wrote:
> It's not clear to me what you are saying. Are you suggesting that edgeR is
> returning a large number of significant genes at a low FDR, or are the
> number of significant genes roughly the same at the same FDR's between the
> two packages?

I don't know if this is the case, but I've seen edgeR giving smaller p-values (and FDR) than DESeq (and voom) on the same dataset...

>> How can I solve this
>> problem?
> Sequence more replicates ;-)

> In DESeq you must be using the "blind" method to estimate over dispersion,
> right? You can imagine how that makes it harder to detect all but the most
> extreme fold changes.

A thing I've not checked yet: is the dispersion estimated by DESeq and edgeR similar? 


Davide Cittaro, PhD

Coordinator of Bioinformatics Core
Center for Translational Genomics and Bioinformatics
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Via Olgettina 58
20132 Milano

Office: +39 02 26439211
Mail: cittaro.davide at hsr.it
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