Hello, I am trying to run a makeConstrasts() function to compute eBayes t- test with the following design list (six hybridizations and three samples -in duplicates): A B C 1 1 0 0 2 1 0 0 3 0 1 0 4 0 1 0 5 0 0 1 6 0 0 1 I would like to compare sample "B-C", so when I run: >contrasts.matrix<-makeContrasts(B-C, levels=design) it works great! However, I have B and C stored in as 'member' (e.g. member[1] = B, member[2] = C). So, when I try to run: member1<-member[1] member2<-member[2] >contrasts.matrix<-makeContrasts(member1-member2, levels=design) I get a following error message: Error in eval(expr, envir, enclos) : object "member1" not found Can you please help me how I can directly compare the content of the 'member' in makeContrasts() function? Thank you, Jay [[alternative HTML version deleted]]