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...alling? This is what I've done: Change dir(to where CEL files are saved) Data <- ReadAffy() eset <- rma(Data) write.exprs(eset, file="mydata.txt") With this I am only able to get the average intensities per gene not the intensity per probe of each gene. Please help me out. Kanan

Dear all I apologize for cross-posting, but first it is accepted custom to thank the repliers and give a summary, and second I have still the feeling that this problem might be a general statistical problem and not necessarily related to microarrays only, but I might be wrong. First, I want to thank Robert Gentleman, Mark Kimpel and Mark Reiners for their kind replies. Robert Gentleman kindly