[BioC] Limma FDR question

[Sean Davis]

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
>
>
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