Hello, 

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.. 

There's several issues in your post.

• If you want to do library size normalization, then don't specify norm.factors in the DGEList call. Having all normalization factors equal to 1 means that edgeR will use the log-library sizes directly as offsets, without calculating effective library sizes.
• It doesn't matter if you skip calcNormFactors or not, your normalization factors should already be 1.
• All currently recommended edgeR pipelines use glmQLFit and glmQLFTest instead of exactTest. The quasi-likelihood GLM framework is more accurate, more flexible and faster than "classic" edgeR - better in every way.