I want to normalise raw read counts obtained from RSEM, using TMM in edgeR.
expr <- DGEList(counts=data)
expr <- calcNormFactors(expr)
I will then obtain rpkm values from this expr object using
expr_norm <- rpkm(expr, log=TRUE, gene.length=gene_length$Length)
For the gene lengths I need to specify, should I use length or effective length from the RSEM output?
Thanks very much