# using Merge lists <- list(eset,eset3) eset_both <- inSilicoMerging::merge(lists, method='NONE') # using combine eset_both2 <- combine(eset, eset3) # Manually neweset<-ExpressionSet(assayData=cbind(exprs(eset),exprs(eset3)[featureNames(eset),])) phenoData(neweset)<-new("AnnotatedDataFrame",rbind(pData(eset),pData(eset3))[sampleNames(neweset),]) # Compare results sum(exprs(eset_both)[featureNames(neweset),sampleNames(neweset)]!=exprs(neweset))/length(featureNames(neweset)) sum(exprs(eset_both2)[featureNames(neweset),sampleNames(neweset)]!=exprs(neweset))/length(featureNames(neweset))