Hi All, I am analyzing the Illumina data and need to add expression intensities in the final results. At this moment output from Limma does not include normalized expression intensities for all samples. I was suggested to use 'Limma2anaaffy' from 'affycoretools' but unfortunately it does not work on Illumina data.Could somebody please suggest me how can I add expression intensities to final output? One way I see it is to get the IDs from final result and than extract expression intensities for those IDs from the normalized data. Finally, I can manually add expression intensities to the final result using Excel. But problem is that in illumina results from 'decideTests' Nu Ids are missing, which are present in expression set. So is there any way to add NuIds to final results? Simplified code: mydata<- lumiR.batch(filename) lumi.N.Q <- lumiExpresso(mydata, normalize.param=list(method='rankinvariant')) sampletype <- c('1','1','2','2','3','3') group <-factor(sampletype) design<- model.matrix(~0+group) fit <- lmFit(esetLumi.Reduced, design) fit2 <- eBayes(fit2) results.default <- decideTests(fit2) write.fit(fit2,results.default,file='RESULTS2.tsv', sep = '\t') Please suggest me how can I add expression intensities to the final result output file? Or at least how can I have nuIDs in my final results? Thanks AK