Limma Voom

Question

[maryak]

Can i use limma voom for differential analysis if data is already TMM normalized?

Answer 1

[ATpoint]

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.