[BioC] FDR/adj.Pvalues

[Naomi Altman]

Have a look at the estimate the pi0 - that can have a big effect.  To 
understand what is going on, look at the histograms of unadjusted 
p-values.  The stronger the peak at the low end, the smaller the 
FDR-adjusted p-values will be.

--Naomi

At 03:54 AM 1/26/2008, Lana Schaffer wrote:
>Hi,
>I have a set of samples for which the FDR/adj.Pvalues (BH)
>are >.5 for the same unadjusted pvalue level and number of
>testing genes as another set of samples.  The other set of
>samples have more significant FDR/adj.Pvalues.  What would
>be some of the reasons why these adjusted pvalues would
>would be different between the 2 sets of samples?
>Lana
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111