[BioC] edgeR logFC

[Ryan C. Thompson]

Looking in the code for glmLRT, I see this line:

logFC <- drop((glmfit$coefficients %*% contrast)/log(2))

Which looks like the formula for changing the logarithm base from e to 
2. So I believe logFC is reported in base 2.

On Mon 14 Jan 2013 05:27:40 PM PST, chris_utah wrote:
> Hello,
>
> I just need someone to clarify whether the logFC column in the toptags dataframe is log base 2 or log base 10.  I was unable to see this information in the manuals.
>
> Thank you very much.
>
> best wishes,
> Chris
>
>
>
>
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