Looks correct. Gordon > Date: Tue, 20 Jul 2010 17:44:07 -0400 > From: HuW at mskcc.org > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] the design matrix again > > > Hi everyone, > > I know my question is answered in some extent on mail list. But I am > still not feel very confidence about my design. I really appreciate if > anyone can help me on this. > > the data set is about the patients before and after treatment. for > example, for 3 patients. I want to find out the genes that changed > expression before and after treatment. if I have 3 patients, I did like > this: > >> design > patient1 patient2 patient3 treatment14 > 1 1 0 0 0 > 2 0 1 0 0 > 3 0 0 1 0 > 4 1 0 0 1 > 5 0 1 0 1 > 6 0 0 1 1 > attr(,"assign") > [1] 1 1 1 2 > attr(,"contrasts") > attr(,"contrasts")$patient > [1] "contr.treatment" > > attr(,"contrasts")$treatment > [1] "contr.treatment" > >> eset.rma.fit = lmFit(eset.rma, design); >> eset.rma.bayes = eBayes(eset.rma.fit); >> topTable(eset4.rma.bayes, coef = "treatment14", adjust = "BH"); > > thank you very much. > > Wenhuo Hu ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}