Friends, Mick Watson was nice enough to help me fix a problem I was having using the kooperberg background correction function and asked me if I wouldn't mind posting a summary of our discussion so that others may benefit. Thanks to Mick for the following help. I was receiving an error message when I tried to run the kooperberg function on my genepix-generated dataset. Despite having gal files that seemed to work with other functions, I would receive one of the following error messages: "Error in getLayout(get(genepixFiles[1])) : gal needs to have columns Block, Row and Column" or "Error in "[.data.frame"(slide, , "F635.Mean") :undefined columns selected" After sending Mick my gal and gpr files, he was able to figure out that my problems were: 1. The example kooperberg script provided under ?kooperberg, which I was using as a template for my own function, has its skip argument set to 26, whereas the data in my gal file started on line 31. 2. I had # characters in my annotation column (e.g. tubulin #6), which R translated as a comment to be ignored. Mick sent the following fix: genepixFiles <- dir(pattern="*\\.gpr$") read.series(genepixFiles, suffix=NULL, skip=31, sep="\t", comment.char="", quote="\"") layout <- getLayout(get(genepixFiles[1])) RGmodel <- kooperberg(genepixFiles, layout=layout) gal <- readGAL("MOB-1-3.anno.gal") RGmodel$genes <- gal the skip and comment.char arguments address these two issues. Thanks Mick! Matt --------------------------------------------- College of Agriculture and Life Sciences Web Mail. http://ag.arizona.edu