Sorry if this is a bit basic for the list, but I've had a few people contact me who struggle to read in OGT arrays using limma. The code below works. If anyone has any trouble, feel free to contact me. Mick # where files is a list of filenames library(limma) RG <- read.maimages(files = files, source = "generic", columns = list(R="rMeanSignal", Rb="rBGMedianSignal", G="gMeanSignal", Gb="gBGMedianSignal"), annotation = c("FeatureNum","Row","Col","ProbeU ID","ProbeName","GeneName","SystematicName","Description"))