Hi Ezhil
Quite possibly. Look at this simple example based on what you describe: > p.adjust(c(0.0002, 0.41, 0.4, 0.42,0.43)) [1] 0.001 1.000 1.000 1.000 1.000 Does this fit what you are seeing? Regards JS --- Web sites: www.ifr.ac.uk www.foodandhealthnetwork.com -----Original Message----- From: A Ezhil [mailto:[EMAIL PROTECTED] Sent: 10 July 2008 16:23 To: r-help@r-project.org; john seers (IFR) Subject: RE: [R] false discovery rate ! Dear John, My P values are not same and the smallest P value = 0.0002. My P value distribution is not that great (see the attached file), most of them are > 0.4. Do you think this is the reason for getting same FDR vlaues? Thanks again, Ezhil --- On Thu, 7/10/08, john seers (IFR) <[EMAIL PROTECTED]> wrote: > From: john seers (IFR) <[EMAIL PROTECTED]> > Subject: RE: [R] false discovery rate ! > To: [EMAIL PROTECTED], r-help@r-project.org > Date: Thursday, July 10, 2008, 8:27 PM Hi > > Are all your input p values the same? If so your output FDR values > would be the same. > > Or are all your p-values relatively large? Then (nearly) all your FDR > values might be 1. > > Why don't you put a small example up of what you did? > Then we could see > what method you used etc. > > Regards > > > JS > > > > > --- > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] > On Behalf Of A Ezhil > Sent: 10 July 2008 15:41 > To: r-help@r-project.org > Subject: [R] false discovery rate ! > > Dear All, > > It is not a typical R question (though I use R for this) but I thought > someone will help me. For the list of P values, I have calculated FDR > using p.adjust() in R (bioconductor). But my FDR values are same for > all the P values. When do we get same FDR values? Does the smallest P > values should less than 1/N? (where N is the number of P values) > > Thanks in advance. > > Kind regards, > Ezhil > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
