Hi List, I am trying to scale (sRNA/degradome) libraries for specific downstream analysis. The analysis is different from finding differentially expressed genes and therefore I might not be using any other function of edgeR. To scale two libraries: files =c('Lib1.txt','Lib2.txt') data <- readDGE(files) factors.TMM <- calcNormFactors(data,method=c("TMM")) factors.TMM This gives me an output: > factors.TMM An object of class "DGEList" $samples files lib.size norm.factors Lib1 Lib1.txt 37075389 0.8146845 Lib2 Lib2.txt 29579135 1.2274690 $counts Lib1 Lib2 TTTTGCATGGCACTGTTTTGACGCT 2 2 GCCGCTCCCGCCGCCGCGAATCCC 1 0 GACCGAATTACACCCCCGAACTTA 3 1 GCAATGCCGCTTGTAAAGCTCTTTCGTCGAGTG 1 0 GCAAATGGTGGCCGGAACTCAGCAC 1 0 16110540 more rows ... I see that the counts above are not 'scaled'. Could you please tell me how can I correct the counts using the 'norm.factors' information? Is there a function that I can use to input 'factors.TMM' and get scaled counts? If not, is it possible to do calculation manually i.e. without R function using the information from $samples? Best AK