I want to calculate RPKM values of my data and, following previous posts, I use the function rpkm() of edgeR. Initially, I checked how the function works on the hypothetical data of http://blog.nextgenetics.net/?e=51 (Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Wagner GP, Kin K, Lynch VJ. Theory Biosci. 2012) and I got as output the "inconsistent" values presented at the second table of "Inconsistency with RPKM" paragraph of the above webpage. Could someone please advice if there is actually a problem with the rpkm() function in edgeR? if yes, do I have to recalculate the values manually or is there an updated function?