[BioC] edgeR logFC

[Gordon K Smyth]

Or else look at the help page for glmLRT, which says:

"The data frame table contains the following columns:
logFC: log2-fold change of expression between conditions being tested."

In edgeR, all fold changes are stored internally in natural log, meaning 
that fit$coefficient valuas are natural log, but all fold changes that are 
presented in output tables or stored in fit$table components are log2.

Best wishes
Gordon

> Date: Mon, 14 Jan 2013 17:32:42 -0800
> From: "Ryan C. Thompson" <rct at thompsonclan.org>
> To: chris_utah <chris.gregg at neuro.utah.edu>
> Cc: bioconductor at r-project.org
> Subject: Re: [BioC] edgeR logFC
>
> 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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