Hello,
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~
Thank you! I agree with you. Someone just gave me the log fold change result from CQN log2 scale data, so I wanted to double-check the result is inappropriately processed.
Hi. You mention here that you use CQN together with limma. Could you maybe share how you do it, I don't think it's a default functionality, as in this post: https://support.bioconductor.org/p/56238/ Do you know any kind of resource that would help me get the two tools working together?
I know I'm resurrecting a very old post, but it's one of the only ones I found googling for using CQN together with limma.