Hi BioC, I have question about LIMMA makeContrasts( ) function. I am reading parameter file for LIMMA from out side R environment and building design matrix. G1 G2 and G3 are Group names coming from parameter file. > Groups <- c("G1","G2","G3"); > colnames(design) <- c(Groups); > design G1 G2 G3 1 1 0 0 2 0 1 0 3 0 1 0 4 0 0 1 5 0 0 1 6 0 0 1 attr(,"assign") [1] 1 1 1 attr(,"contrasts") attr(,"contrasts")$"factor(c(mask))" [1] "contr.treatment" > fit <- lmFit(myRMA,design); upto here it works great. now, when I do, > makeContrasts(Groups[1]-Groups[2],levels = design); Error in Gs[1] - Gs[2] : non-numeric argument to binary operator has anyone came across this sort of problem? or may be I am doing something wrong..? any suggestions? Saurin -- |------------------------------------------------ | Saurin Jani,MS | Statistical and Research Analyst | | Department of Cell Biology and Anatomy | Medical University of South Carolina (MUSC) | 173 Ashley Ave | Charleston,SC - 29407 (US) | | Email: jani@musc.edu | Phone: (843)792-5483 |------------------------------------------------