Thank you Sean. Now I am clear how limma handle multiple correction with 
multiple correction. It's using "separate" mode.
decideTests() source code clearly show this.
Thank you.

Regards,
Xiaokuan




________________________________
From: Sean Davis <sdavis2@mail.nih.gov>

Cc: bioconductor <bioconductor@stat.math.ethz.ch>
Sent: Mon, September 27, 2010 1:39:11 PM
Subject: Re: [BioC] applying p.adjust() in limma






Dear List,
>
>Sorry to bring up this adjusted p value question about limma. I searched mail
>list but didn't find an answer.
>
>I know limma use "p.adjust()" for multiple test correction. And if there is 
only
>one coefficent, the adjust p values results of limma's top table is the same as
>I directly apply p.adjust to the P.Value vector.
>
>My question is that if we have several coefficent, for example, 3 comparisons,
>how does limma use the p.adjust()?
>I tried to feed p.adjust() as: p.adjust(tp$P.Value,
>method="fdr",n=length(tp$P.Value) * 3), but the results are different from the
>tp$adj.P.Val.
>
>Could some let me know how limma apply p.adjust() to handle this situation
>(several comparisons/coefficents)?
>
>

Hi,  Xiaokuan.

See the help for decideTests().

Sean



      
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