I am performing differential expression of 10 paired samples (cancer and normal tissue) in edgeR and I'm following '3.4.1 Paired samples' in the Bioconductor User's Guide.
Do the library sizes need to be normalised prior to testing for treatment efftect?
y <- calcNormFactors(y)
Estimating dispersion, fitting to a linear model and testing for treatment effect.
y <- estimateDisp(y,design) fit <- glmQLFit(y, design) qlf <- glmQLFTest(fit) topTags(qlf)
I don't get any differentially expressed genes after I normalise, but if I omit normalisation I get differentially expressed genes.