10 Dec 13:50 2004

### Re: Limma FDR question

See ?p.adjust for specifics. However, in a particular case, if one has 100 genes with fdr less than 0.05, then 5 out of that 100 are expected to be false positive. In other words, for any given fdr cutoff x, if there are N genes with fdr<x, then x*N genes are expected to be false discoveries. Sean On Dec 10, 2004, at 7:21 AM, M PEREZ wrote: > > Hi all, > > I was wondering how the p-value correction using fdr works. > > The following Limma package's command " topTable(fit,number=100, > adjust="fdr")" corrects the p-values but I don't know which is the > percent of false positive we can expect using this correction. Is the > FDR fixing at one pre-determined value, e.g. 5 %? > > Thank you in advance > > Best, > > Manuel > > > > --------------------------------- >(Continue reading)