Hi, Due to memory limitation, I have to split my dataset and analyze subsets of CEL files separately, so I have several AffyBatch and ExprsSet objects. My questions is how do I use the methods provided by the affy package to normalize (quantile, loess) between chips in different ExprsSets? Many thanks in advance, -Rani. [[alternative HTML version deleted]]

Rani, If you want the standard rma normalisation then you could try eset <- rma(data) or justRMA() which I think use less memory than expresso so you might be able to do them all at once. Alternatively perhaps RMAexpress for windows, this seems to perform well on 256RAM with c.25chips. http://www.stat.berkeley.edu/~bolstad/RMAExpress/RMAExpress.html Hope this is useful. Matt