Hi all, I am trying to convert RMA normalized intensity values in my matrix (generated from Affymetirx raw .CEL data composed of ~30 tumor samples and 7 normal samples) to log ratios in which the intensity values from each tumor sample are compared with a reference sample (in this case I chose one of my normals). I was told that I could use a function like > log(eset/esetRef,2) to generate the new matrix containing log ratios. I have reduced my data using a general filter to remove low signal and low variance: > dim(esetSubNat) [1] 1470 36 > dim(esetSubRef) [1] 1470 1 When I try this log function I get the following error: > esetSubLog <- log(esetSubNat/esetSubRef,2) Error in esetSubNat/esetSubRef : non-conformable arrays Can anyone give me any idea where I am going wrong or how else I might try to generate the log ratios? Thank you, Mark http://sites.google.com/site/lfmmab/ [[alternative HTML version deleted]]