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Hi if I understand you rightly you want to know how to get each contrast 6H-0H and 24H-6H. or A and B as you say. contrasts.fit will have worked out both. The easiest way to access is using toptable and either select A or B using coef=1 or coef=2 e.g. toptable(fit2, coef=1, adjust.method="fdr") or toptable(fit2, coef=2, adjust.method="fdr") Is that what you mean? Stephen Henderson Wolfson Inst. for Biomedical Research Cruciform Bldg., Gower Street University College London United Kingdom, WC1E 6BT +44 (0)207 679 6827 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of gregory voisin Sent: 13 June 2006 15:14 To: bioconductor Subject: [BioC] understanding of makeContrats() in Limma Hi Bioconductorians, In this time ,as reference documentation, i use a web doc: 23. Limma : Linear Models for microarray data ( Of course , written by G.Smith) In section 23.11 , Time Course experiments, treated analyse the same way that estrogen data.. but with some difference : Gordon write :" which gene respond at either the 6 h OR 24 h. times in the wt?" code: >cont.wt = makeContrasts("wt.6h-wt.0h", "wt.24h-wt.6r", levels =design) #build a contraste matrice. > fit2 = contrasts.fit (fit , cont.wt) >fit2 = eBayes (fit2) To Choose Interesting Genes sel.wt = p.adjust(fit2$F.p.values, method = "fdr") < 0.05 PROBLEM OF UNDERSTANDING HERE: in the question "which gene respond at either the 6 h OR 24 h. times in the wt", it's set A OR set B and to choose interesting genes , there is not distinction between A and B. Hence : May be that the OR ( use here) is inclusive ( Include the AND) => logical OR, by consequently, sel.wt give me the set of DEG (differential Expressed Genes) at 6 h and 24 h... Am I OK or OutSide.??? Thamks for your Help.. Greg Voisin Bioinformatician Centre de recherche du CHUM . Montreal [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}