I am trying to correct for the effect of 2 covariates in a gene expression data set.
design<-model.matrix(~0 + Factor + cov1 + cov2) QUESTION: How to set up the contrast matrix? The usual commands fit <- lmFit(selDataMatrix, design) cont.matrix <- makeContrasts(FacCont=Group1-Group2, levels=design) fit2 <- contrasts.fit(fit, cont.matrix) does not work because the original design matrix includes the covariates. I think I don't really understand how the contrast matrix works. John W. Belmont, M.D.,Ph.D. Professor Department of Molecular and Human Genetics Baylor College of Medicine 1100 Bates, Room 8070 Houston, TX 77030 713-798-4634 fax: 713-798-7187 ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
