Hey everyone, I'm using Rockhopper to do my RNAseq analysis, with 3 conditions and biological triplicates. I'm quite in doubt of how is made the normalization and expression calculation? For the final expression of each gene, looks that they use the total of the reads of the biological triplicate to calculate the expression, wouldnt be average? Thanks, Brenda
What do the expression values for each transcript correspond to?
Expression values reported by Rockhopper for each transcript in each condition are similar to RPKM (reads per kilobase per million mapped reads) values. However, RPKM values are generally normalized by the total mapped reads, whereas the expression values reported by Rockhopper are normalized by the upper quartile of gene expression, which is a more robust normalizer.