Limma Voom
1 answer
If with "TMM-normalized" you are referring to raw counts that were produced by calcNormFactors() and then cpm(x, log = TRUE) from edgeR, then you could use limma.trend, please see the limma user guide for details. Limma-voom itself starts from raw counts, whereas limma-trend can directly use normalized counts on log2 scale.
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