Hello all, I am working with a series of expression arrays (in gpr formats generated by GenePix) to find DE genes. I wish to incorporate Spot Types File like in the demos in Limma manual, but I don't know how to go about generating such file. To be more specific, how do I find out what are all the possible types of spots in my dataset? Below is basically my codes of what I have so far, up to the part before creating design matrix. #load in target file targets<-readTargets("spleen_target_file.txt") #Iignore anything < -50. f <- function(x) as.numeric(x$Flags > -50.5) RG <- read.maimages(targets, source="genepix", wt.fun=f) #Background correction #It was reported that for assessing DE, use normexp with offset, get better result than using simple background subtraction RG_bc <- backgroundCorrect(RG, method="normexp", offset=50) #LOESS normalization MA <- normalizeWithinArrays(RG_bc) Thanks! Casper [[alternative HTML version deleted]]