EdgeR GLM following voom conversion of counts
1
0
Entering edit mode
@adamptaranto-9720
Last seen 8.1 years ago

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?

limma voom edger rnaseq • 1.1k views
ADD COMMENT
1
Entering edit mode
@ryan-c-thompson-5618
Last seen 7 months ago
Scripps Research, La Jolla, CA

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 COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 645 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6