TMM followed by inverse normal transform

TMM followed by inverse normal transform


Hey all,

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.

I used 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 cpm, 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.





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