Thank you, Gordon.  I appreciate you helping to clarify this for me.

best wishes,
Chris


On Jan 15, 2013, at 4:30 PM, Gordon K Smyth wrote:

> 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@thompsonclan.org>
>> To: chris_utah <chris.gregg@neuro.utah.edu>
>> Cc: bioconductor@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
>>> 
> 
> ______________________________________________________________________
> The information in this email is confidential and inte...{{dropped:25}}

