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

[Davide Cittaro]

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 ;-)
> 

ROTFL!
> 
> 
> 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? 

d



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