> 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. new_object=decideTests(result_of_eBayes,method="global",adjust.method= "BH",p.value=0.05) Best Regards, Maciej Jo?czyk, 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