4 weeks ago by
Vienna - BOKU
which package in R should i use for Differential gene expression?
Assuming you mean to do diff.expr. with FPKM, I think Limma does a pretty good job. However ...
among many packages which package is better?
This question I think is hard to answer. The jury is out on this one!
is DGE using raw count is better or using FPKM/RPKM normalized counst are better ?
The author of the FPKM measurements himself called FPKM as "biased" and "wrong". So I would go for raw counts when possible. My pipeline usually includes htseq-count and DESeq2, but other couting programs and other differential expression analysis programs are fine!