I would like to use only the lib size as normalizing factor in edgeR, so I am doing this:
cds <- DGEList(counts = counts, group = group, norm.factors = MyNormFactors)
I skip the
cds <- calcNormFactors(cds, method = "none")
Because It will bring the norm factor back to 1..
and I continue with calculating dispersion and doing the exact test.
What is seems to me strange is that the pseudo count look the same as the original count.
Isn't it supposed to change?
When I use no normalization (factor = 1) the pseudo count do change a little..
Just want to know if this is the right way so I could trust my results..