[BioC] Limma and negative p-values
naomi at stat.psu.edu
Thu Mar 15 16:37:49 CET 2012
I have posted this several times, but it has been a while so I will
do it again.
Suppose p=.001 and you have 10000 genes. Then you expect 10
significant genes just by chance. So if you observe 9 or 10
significant genes at this level, your FDR should be 100%. If you
observe 11, your FDR should be about 10/11=0.91. Etc.
This does not mean that you don't have any significant genes. It
means your experiment did not have enough power to detect them.
At 10:31 AM 3/15/2012, Ovokeraye Achinike-Oduaran wrote:
>Excuse the language but I say shady because they all range from
>~0.918 - 0.999.
>On Thu, Mar 15, 2012 at 3:54 PM, Steve Lianoglou
><mailinglist.honeypot at gmail.com> wrote:
> > Hi,
> > On Thu, Mar 15, 2012 at 9:50 AM, Ovokeraye Achinike-Oduaran
> > <ovokeraye at gmail.com> wrote:
> >> Hi all,
> >> Sorry...a recall of my previous mail...the p-values are fine(or not)
> >> but not negative...the corrected p-values, however, look very shady.
> >> Any suggestions there?
> > Shady?
> > Need to elaborate, please.
> > -steve
> > --
> > Steve Lianoglou
> > Graduate Student: Computational Systems Biology
> > | Memorial Sloan-Kettering Cancer Center
> > | Weill Medical College of Cornell University
> > Contact Info: http://cbio.mskcc.org/~lianos/contact
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