
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
 		 	   		  
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