Hi all I've got the file test.R with the following code: filenames <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", "1M1W050304.CEL", "1M3W050304.CEL") filepath <- "/net/array/WormDystrophy" samples <- c("1M2W050304.CEL", "2M2W050304.CEL", "3M2W050304.CEL", "1M1W050304.CEL", "1M3W050304.CEL") custom <- c("rma", "quantiles", "pmonly", "medianpolish") log2trans <- TRUE library(affy) library(gcrma) library(vsn) bgcorrect.methods <- c(bgcorrect.methods, "gcrma") normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn") express.summary.stat.methods <- c(express.summary.stat.methods, "rlm") setwd(filepath) exprset <- rma(ReadAffy(filenames = filenames)) I run it in batch mode from the linux command line with "R --no-save < test.R". Everything is ok, except when executing the last line. The rma() runs fine with the usual output: Background correcting Normalizing Calculating Expression But then it comes with the error: Error in rma(ReadAffy(filenames = filenames)) : dimnames applied to non-array Execution halted This is REALLY weird because: 1) It runs well in an interactive session just by copying and pasting the code from the test.R file 2) It works fine if I change the order in which the file names are given!! Any ideas what the error means or what might be happening here? (I'm on RedHat9, R 1.8.1, affy 1.3.28) Thanks Jose