Greetings, I have masked 168 probe pairs and then run RMA and Alot of the expression values have come out NA. I am concluding that RMA is not calculating the expression values for probesets which contain masked probepairs. Is this a correct conclusion? abatch <- bg.correct.rma(abatch0); msk <- scan(filename, skip=0, list("", "")) for (i in 1:length(msk[[1]])) { nam <- msk[[1]][i]; txt <- gsub("-", ":", msk[[2]][i]); lst <- eval(parse(text=paste("c(", txt, ")"))); #list if (i == 1) { ids <- pmindex(abatch, nam)[[1]][lst]; } else { ids <- c(ids, pmindex(abatch, nam)[[1]][lst]); } ids <- c(ids, mmindex(abatch, nam)[[1]][lst]); } intensity(abatch)[ids, ] <- NA; eset2 <- rma(abatch,background=F); Thanks for any help. Lana [[alternative HTML version deleted]]