Hi all, Sorry if this is a basic thing that I am not seeing. I have looking again and again at this but I dont know what is going on here, I am trying to read my controls into my ma Layout, and look if it is reading them properly. These are the commands I am using: I am using read.GenePix() to read gpr files. I made my controlCode with: controlCode <- as.matrix(read.table("controls.txt", sep="\t",header=TRUE, quote="\"", fill=TRUE)) I am trying to put my controls in maLayout, by doing: maControls(testRapa@maLayout) <- maGenControls(Raw@maGnames@maInfo, id="Name") because my identifiers are in Name column. Some of the genes I have in my name column are alien9, alien 10, HUMPPARP1+/-5' HUMPPARP1+/- I dont have HUMPPARP1NC as an identifier in my Name columns. When I have a control code like this: controlCode Pattern Name 1 "alien9" "con" 2 "alien10" "con" 3 "HUMPPARP1NC" "con" It doesnt see alien9 or alien10, but it sees: HUMPPARP1+/-5' HUMPPARP1+/- When my control code is: Pattern Name 1 "alien9" "con" 2 "alien10" "con" 3 "HUMPPARP1+/-" "con" It doesnt label any of those genes as controls, even if they are there I have created controls.txt with Xmacs and with excel. I dont think that there are spaces in the names that may be doing that. Any suggestions? Thanks a lot. Inma