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) gives an error message because the original design matrix includes the covariates. Error in contrasts.fit(fit, contrast.matrix) : Number of rows of contrast matrix must match number of coefficients In addition: Warning messages: 1: In rn != cn : longer object length is not a multiple of shorter object length 2: In contrasts.fit(fit, contrast.matrix) : row names of contrasts don't match col names of coefficients 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 [[alternative HTML version deleted]]