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Question: EdgeR GLM following voom conversion of counts
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gravatar for adam.p.taranto
2.6 years ago by
adam.p.taranto0 wrote:

Documentation for limma-voom analysis of RNA-seq data uses eBayes to perform pairwise differential expression tests. For more complex experimental designs, would it be reasonable to use edgeR's GLM method to call DE genes from dge objects containing voom transformed counts?

ADD COMMENTlink modified 2.6 years ago by Ryan C. Thompson6.8k • written 2.6 years ago by adam.p.taranto0
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gravatar for Ryan C. Thompson
2.6 years ago by
The Scripps Research Institute, La Jolla, CA
Ryan C. Thompson6.8k wrote:

LImma can already accomadate any design matrix that edgeR can. It definitely doesn't make sense to use edgeR on voom-transformed counts, because edgeR models values on a raw count scale, and voom performs a transformation to logCPM.

ADD COMMENTlink written 2.6 years ago by Ryan C. Thompson6.8k

Indeed, voom will happily generate negative log-expression values when the counts are low relative to the library size. It would be completely nonsensical to try to treat such values as counts in an edgeR analysis.

ADD REPLYlink written 2.6 years ago by Aaron Lun21k
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