I am trying to use DESeq2 to convert raw counts to fpkm, so I can compare gene aboundance across genes and not only across samples. I have a couple of questions on how to do so:
- Should I first normalize the counts and transform them with vst and then use the
fpkm()function, or should I simply input the raw counts and the
fkpm()function will then take care of normalization as well?
- How do I make sure that the genes in my
GRangesobject containing the gene lengths match the genes in the