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
[[alternative HTML version deleted]]
Looking in the code for glmLRT, I see this line:
logFC <- drop((glmfit$coefficients %*% contrast)/log(2))
Which looks like the formula for changing the logarithm base from e to
2. So I believe logFC is reported in base 2.
On Mon 14 Jan 2013 05:27:40 PM PST, chris_utah wrote:
> Hello,
>
> I just need someone to clarify whether the logFC column in the
toptags dataframe is log base 2 or log base 10. I was unable to see
this information in the manuals.
>
> Thank you very much.
>
> best wishes,
> Chris
>
>
>
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
Or else look at the help page for glmLRT, which says:
"The data frame table contains the following columns:
logFC: log2-fold change of expression between conditions being
tested."
In edgeR, all fold changes are stored internally in natural log,
meaning
that fit$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
>>
______________________________________________________________________
The information in this email is confidential and
intend...{{dropped:4}}
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}}
