I am trying to find in the documentation of edgeR where it says the default base of the log function. I've used exactTest and topTags it gives me logFC but is it base e, 2, or 10?
It's log2 in all common RNAseq differential expression programs, including edgeR. The reason for that is that counts can range from 0 to infinity, so using a log2 transform allows running the MLE optimization in (-infinity, infinity), which is simpler and better for fold-changes <1.
I'm not sure this is an explanation for why log2 is taken instead of log10 or the natural log. Indeed, I'm fairly sure that the coefficients that are stored in the fits in edgeR use the natural log, consistent with most GLM approaches; it's only when converting to human readable form that the base is shifted from e to 2
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
version 2.3.6
DE analysis by edgeR
I read here that is likely base e 2
DE analysis by edgeR
I read here that is likely base e 2
It's definitely 2 in the topTags