I tried to normalize my data in edgeR as instructed in the respective vignette. I calculated CalcNormFactors and then proceeded with estimating the dispersion as usual. However, when I visualized my data in a boxplot, they still look the same as the unnormalized. My dataset was a single factor experiment with 4 different levels. So, my question is: does CalcNormFactors simply calculate the size factors to be applied to the different libraries or does it actually normalize them? I therefore wondered whether one should apply a cpm or another method on top or not.