Dear list members, I wanted to compare rma and vsn for Affy data as I ran into a data set where rma could be improved (the t-statistic was still intensity dependent). Everything except the normalization method from rma I wanted to stay the same to see if vsn outperforms quantile normalization. I posted a question on how to use expresso() with vsn befor and thanks to a thorough discussion with Wolfgang Huber I managed to put up a script. I had to change the median polish function as it log transforms the data in the original affy package. This is the script that performed well (results very similar to rma) in the Affymetrix latin square data set: generateExprVal.method.medianpolish2 <- function(probes, ...) medianpolish2(probes, ...) medianpolish2 <- function(x, ...){ tmp <- medpolish(x, trace.iter=FALSE, ...) ##rough estimate sigma <- 1.483*median(abs(as.vector(tmp$residuals)))/sqrt(nrow(x)) list(exprs=tmp$overall + tmp$col,se.exprs=rep(sigma, ncol(x))) } generateExprSet.methods <- c(generateExprSet.methods, "medianpolish2") express.summary.stat.methods <- c(express.summary.stat.methods, "medianpolish2") normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods,"vsn") es5 = expresso(data, pmcorrect.method = "pmonly", bgcorrect.method = "rma", normalize.method = "vsn", summary.method = "medianpolish2") Of course, there might be other summary or background correction methods than these, but as the results are very close to rma, there won't be much room for improvement. So, if you ask me, this would be the script to use for affy chips with vsn normalization with the current bioconductor version. Any comments? Oh, in case if you are wondering: I couldn't try vsn with the data set I mentioned at the beginning - it's to big to calculate vsn on my PC, but as soon as I get my new one I'll try... Details of the comparisson of VSN to RMA and MAS can be found at my web page: http://staff-www.uni-marburg.de/~hartmann/ Thanks a lot to Wolfgang and all those that answered, too. -oli- -- Oliver Hartmann, Institute of Medical Biometry and Epidemiology Philipps-University Marburg, Bunsenstr. 3, D-35037 Marburg phone +49(0)6421 28 66514, fax +49(0)6421 28 68921