[BioC] FDR/adj.Pvalues

Naomi Altman naomi at stat.psu.edu
Mon Jan 28 00:31:09 CET 2008

Since every experiment has false discoveries and false 
nondiscoveries, you should use time type of confirmatory method to 
determine if these genes are differentially expressed.


At 12:30 PM 1/27/2008, Lana Schaffer wrote:
>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?
>From: Naomi Altman [mailto:naomi at stat.psu.edu]
>Sent: Sat 1/26/2008 6:50 AM
>To: Lana Schaffer; bioconductor at 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.
>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
> >
> >         [[alternative HTML version deleted]]
> >
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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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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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