[BioC] [DESeq] p-value vs adjusted p-value
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
> 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
Ospedale San Raffaele
Via Olgettina 58
Office: +39 02 26439211
Mail: cittaro.davide at hsr.it
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