Add TMM normalization - Githubissues

QuackenbushLab / NetworkDataCompanion

An R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo

GNU General Public License v3.0

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Closed katehoffshutta closed 2 years ago

katehoffshutta commented 2 years ago

Per group decision, TMM normalization is best for avoiding spurious correlations. We need to add this as a (default) option

FischerJoBio commented 2 years ago

I implemented it (not as the default, not convinced TMM is generally good) through commit 53e046a8b229ed13815f19f1465b8956ef031c4b.

Implemented TMM+CPM normalization as provided by edgeR. New function is logCPMNormalization which does TMM+CPM normalization as suggested by literature.
Rewrote function (and description) of filter genes to be more general as filterGenesByNormExpression.