I am following a protocol from a paper that uses the following pre-processing procedure:
a. Read counts were normalized between samples using TMM (Robinson, M. D. & Oshlack, A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 11, R25 (2010)).
b. Expression values for each gene were inverse normal transformed.
edgeR::calcNormFactors to normalize library size via TMM for part a, but I am confused on how to apply an inverse normal transform on my read counts together with my normalized library sizes. What is my misunderstanding? I know that I can apply other transforms like
rpkm, etc., to the results of
calcNormFactors, and it will transform using the normalized library sizes -- is there a similar function for inverse normal transformation?
Appreciate any help.