Hi, Lana, There are two points to be cared in this procedure. One is that probe-masking should be done after the quantile normalization. RMA quantile normalization does not provide what you want if there are some NA values. The other point is to specify "na.rm=TRUE" in the step of summarization. Unfortunately, current version of C-coded rma() function does not support na.rm option (correct?). Instead of rma() you can use computeExprSet() command. In summary, the following script will be your help, I hope. Now I present my masking script in the form of a function. # # mask.R # # x: AffyBatch object # mfile: maskfile name # mask <- function(x, mfile, skip=2) { m <- scan(mfile, skip=skip, list("", "")) ids <- array(0, 0) for (i in 1:length(m[[1]])) { pname <- m[[1]][i] plist <- gsub("-", ":", m[[2]][i]) parray <- eval(parse(text=paste("c(", plist, ")"))) ids <- c(ids, pmindex(x, pname)[[1]][parray]) ids <- c(ids, mmindex(x, pname)[[1]][parray]) } intensity(x)[ids,] <- NA return(x) } ## ## RMA with NA values ## ## abatch0 <- ReadAffy() abatch1 <- bg.correct.rma(abatch0) abatch2 <- normalize.AffyBatch.quantiles(abatch1) abatch3 <- mask(abatch2, "a.msk") eset <- computeExprSet(abatch3, pmcorrect="pmonly", summary.method="medianpolish", summary.param=list(na.rm=TRUE)) ### END of script ### Try this one! > Hi, > I have tried masking particular probepairs with mas5, expresso,and > computeExprSet, but find in all cases that the probesets with the > masks get "NA" expression values. > In other words, I am unable to mask probepairs without masking the > whole probeset. > Earlier mail seemed to indicate that the masked probepairs worked. > Does anyone think that I am doing something wrong? > > With RMA I get some NA's but do get some probeset expression values. > Thanks, > Lana > _______________________________________ Takatoshi Kawai, Ph.D. Senior Scientist, Bioinformatics Laboratory of Seeds Finding Technology Eisai Co., Ltd. 5-1-3 Tokodai, Tsukuba-shi, Ibaraki 300-2635, Japan TEL: +81-29-847-7192 FAX: +81-29-847-7614 e-mail: t-kawai@hhc.eisai.co.jp