[BioC] about: p.value, adj.p.val, F.p.value

Weiwei Shi helprhelp at gmail.com
Mon Nov 27 18:46:58 CET 2006

Hi, Yan Jun:

You can check some infomation on the multiple testing correction, BH
represents Benjamini & Hochberg (1995) method, which defines a
sequential p-value, a procedure that controls expected FDR.

you probably need to do some literature reading to understand why
multiple testing procedure is neccessary.



On 11/27/06, yanju <yanju at liacs.nl> wrote:
> Dear all,
> I am just a little bit confused about p.value, adj.p.value and
> F.p.value. Could somebody tell me what are the proper cases to use them?
> I am supposed to detect the differenct expressed genes with the p-value
> less than 0.05, therefore, my code is like follows:
>     fit<-eBayes(fit)
>     selected<-p.value<0.05
> But in Limma user guide, the code is like this:
>     selected<-p.adjust(fit$F.p.value, method="BH") <0.05
> here the F.p.value is used.
> And also if i choose the top10 different expressed genes like this:
>     topTable(fit, adjust="BH")
> there is a adj.p.value.
> So I really want to know when to use which. Expecting your reply.
> Regards,
> Yanju
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Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

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