Recently, I have tried to apply GOSeq to RNA-seq expressions after voom adjustment. It has just ocurred that differential expression and gene length were negatively correlated, what is unexpected. I was wondering how much of the gene length impact on Differential Expression Analysis is already removed when using voom. Can someone point me to literature regarding this issue ?
Is cqn normalization method not desirable (it takes into account gene length and GC content) then? Thanks
No, cqn does not remove gene length bias in DE power. Trying to remove that is not even a sensible thing to try to do.