As many of you do, I apologize for asking a likely dumb question, but I appreciate in advance any clarification from you. As far as I know, calcNormFactors() produces two columns of information. The first is lib.size and the second is norm.factors, which multiplying these two columns together gives us an effective library size. However, I don't understand how the normalization factor was calculated, could you please explain me in a simple way as I'm basically a biologist?
From what I read, I understand that TMM_count = raw_counts / ( libsize * norm.factor ). Please kindly let me know what is differences between TMM_count and FPKM values in terms of normalization by library size?