[BioC] Questions about model matrix, logFC and adjusted P.value of t-test

Maciej Jończyk mjonczyk at biol.uw.edu.pl
Wed Oct 27 12:44:02 CEST 2010

> Message: 37
> Date: Wed, 27 Oct 2010 00:52:22 +0200
> From: Mingkwan.Nipitwattanaphon at unil.ch
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Questions about model matrix,	logFC and adjusted
> 	P.value of t-test
> Message-ID: <4cc75ba6.64.1ec.786541259 at unil.ch>
> Content-Type: text/plain; charset="iso-8859-1"

> My result file contains coefficients of all the 16 contrasts
> that I asked for and
> the p-value of each contrast (each t-test) but NOT the
> adjusted p-value. It also
> gives me the F value and the p-value of the F-test and again
> NOT the adjusted p-
> value of the F-test.
> I can get the adjusted p-value from the F-test by using the
> command "p.adjust"
> but not with the t-test. When I used the command "topTable"
> with coeff=1 (until
> 16 each time for all of my 16 contrasts), I can get the
> adjusted p-value of each
> contrast.
> My questions are:
> 1. Why does not the command "eBayes" give adjusted p-value?
> Is there an easier or
> more direct way to get adjusted p-value of the t-test?
Hi Mingkwan,

try "decideTests" command, it allows you to choose multiple contrast
correction method and p-value cutoff. Below example, but read about it
in limma's manual.


Best Regards,

Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1

NOCC, http://nocc.sourceforge.net

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