**30**wrote:

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`

?

Question: Is logFC in edgeR base e, 2, or 10?

0

O.rka • **30** wrote:

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`

?

4

Devon Ryan ♦ **77k** wrote:

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.

`fit`

s 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

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DE analysis by edgeR

I read here that is likely base e 2

3.0kDE analysis by edgeR

I read here that is likely base e 2

3.0kIt's definitely 2 in the topTags

3.0k