I was wondering whether it is always preferable to recalculate the library sizes of your samples after any filtering. I have seen from the manual that this is recommended after filtering out lowly expressed genes, however I was wondering if you would also recommend this after filtering to retain only protein-coding genes? Could this not end up skewing the results if some of your samples had high expression of non-protein-coding genes?
The section of code that I am referring to is:
y <- y[keep, , keep.lib.sizes=FALSE]
Many thanks for the advice,