On Feb 3, 2013, at 12:57 AM, Gordon K Smyth <smyth at="" wehi.edu.au=""> wrote: > Dear Davide, > > The short answer is that you shouldn't be interpreting the fit3 results > because they are probably not want you want. > > You have fitted a linear model in which there is no intercept, but instead > three coefficients representing the means of the three groups. If you > simply display the results of topTable(fit3), then limma will test whether > any of the coefficients are equal to zero. This will select genes that > have mean log-intensities in any group greater than zero. So you are > simply getting a list of highly expressed genes, not genes that are > differently expressed between your groups. > Thanks, that's much clearer now d > Best wishes > Gordon > > >> Date: Fri, 1 Feb 2013 22:12:35 +0100 >> From: Davide Cittaro <cittaro.davide at="" hsr.it=""> >> To: "bioconductor at r-project.org" <bioconductor at="" r-project.org=""> >> Subject: [BioC] What does this mean in Limma? >> >> Hi all, > >> I'm performing an analyis in limma with 3 groups. Normally I would set >> up a simple analysis with 3 contrasts: >> >> groups <- factor(c(A,A,A,B,B,B,C,C,C)) >> design <- model.matrix(~0+group) >> contrasts <- makeContrasts(B-A, C-A, C-B, levels=design) >> fit <- lmFit(y, design) >> fit2<-eBayes(contrasts.fit(fit, contrasts)) >> >> Because of an error, I've didn't set the matrix and performed >> >> fit3<-eBayes(fit) >> >> In which way I should interpret the results in fit3 (which, by the way, >> are really interesting)? >> >> Thanks >> >> d >> > > ______________________________________________________________________ > The information in this email is confidential and intended solely for the addressee. > You must not disclose, forward, print or use it without the permission of the sender. > ______________________________________________________________________ /* Davide Cittaro, PhD Coordinator of Bioinformatics Core Center for Translational Genomics and Bioinformatics Ospedale San Raffaele Via Olgettina 58 20132 Milano Italy Office: +39 02 26439140 Mail: cittaro.davide at hsr.it Skype: daweonline */