I am pretty much new to RNA-seq and wanted to ask a really basic question about differential expression analysis.
I have a set of CQN (conditional quantile normalization) normalized RNA-seq RPKM data (the are all matched-pairs like tumor vs. normal).
When we compare expression of a gene with control, we usually use a log-based fold change like log2(T/N). However, CQN values are already log2 based. So calculating a log-based fold change seems like taking logarithm twice.
So, in this case, do we still take a log fold-change? or do different things like just using differences of those values?
Thank you all~