Thanks.
In the experiment where pi0 is probably smaller and the FDR
is high, some of the genes are plausable for the experiment.
In other words, the unadjusted pvalue is small but the FDR is
high for those genes and those genes are relavent to the experiment.
What do you say about those genes?
Lana

________________________________

From: Naomi Altman [mailto:naomi@stat.psu.edu]
Sent: Sat 1/26/2008 6:50 AM
To: Lana Schaffer; bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] FDR/adj.Pvalues



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




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