Dear affy developer, the function pmcorrect.mas has pm.corrected <- applycbindpps.pm - pps.im, delta), 1, max) It would be clearly more efficient to replace this with one of the following proposals: ## slightly faster pm.corrected <- pmaxpps.pm - pps.im, delta) ## clearly faster pm.corrected <- pps.pm - pps.im pm.corrected[pm.corrected < delta] <- delta ## fastest pm.corrected <- pmax.intpps.pm - pps.im, delta) ####################### ## Timing x <- rnorm(20) y <- rnorm(20) delta <- 0.01 t1 <- system.time(for(i in seq_len(1e5)) apply(cbind(x - y, delta), 1, max) ) t2 <- system.time(for(i in seq_len(1e5)) {z <- x - y; z[z < delta] <- delta} ) t3 <- system.time(for(i in seq_len(1e5)) pmax(x-y, delta) ) t4 <- system.time(for(i in seq_len(1e5)) pmax.int(x-y, delta) ) t1/t2 t1/t3 t1/t4 This change does really decrease computation time, as function pmcorrect.mas is called very often. Assume an Affybatch with N arrays where each array has M different IDs. Then pmcorrect.mas is called N x M - times. Best regards, Matthias -- Dr. Matthias Kohl www.stamats.de