Dear list, I am using EdgeR to calculate differentially expressed genes of RNAseq data. the toptags output gives me both a p-value and an FDR value. is the FDR the 'adjusted p-value' as it is commonly called? I tried to look this up in the archive, but I'm still not completely sure if this is correct. Regards, Kaat De Cremer

Hi, On Thu, Nov 29, 2012 at 5:37 AM, Kaat De Cremer <kaat.decremer at="" biw.kuleuven.be=""> wrote: > > Dear list, > > > I am using EdgeR to calculate differentially expressed genes of RNAseq data. > the toptags output gives me both a p-value and an FDR value. > is the FDR the 'adjusted p-value' as it is commonly called? > I tried to look this up in the archive, but I'm still not completely sure if this is correct. Right, see ?topTags Unless you've changed the call to topTags, you're simply running R's `p.adjust` method on the nominal p-values using the "BH" correction (see ?p.adjust for more info on that). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact