6.8 years ago by
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
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
In edgeR, all fold changes are stored internally in natural log,
that fit$coefficient valuas are natural log, but all fold changes that
presented in output tables or stored in fit$table components are log2.
> 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
> 2. So I believe logFC is reported in base 2.
> On Mon 14 Jan 2013 05:27:40 PM PST, chris_utah wrote:
>> I just need someone to clarify whether the logFC column in the
>> 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,
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