Hi everyone, I'm trying to get affymetrix expression values using three different functions: expresso, mas5 and threestep. Using expresso: eset<- expresso(object, bgcorrect.method = "mas", pmcorrect.method = "mas", normalize = FALSE, summary.method = "mas") eset<-affy.scalevalue.exprSet(eset) exprs(eset)<-log2(exprs(eset)) Using mas5 eset<-mas5(data) exprs(eset)<-log2(exprs(eset)) But I have no idea how to get into this using threestep. I've tried: eset<-threestep(data,background.method="MAS",normalize.method="scaling ",summary.method="tukey.biweight") But the results are quite different to the ones given by mas5 and expresso (which are exactly the same between them). I know that threestep returns log2 values... Any tips?? Thanks in advance, Javier