[BioC] FC calculation in Limma

[Lana Schaffer]

Kasper,
How do you tell customers that the fold-change is not the
Average of X divided by the average Y signal?
Lana

-----Original Message-----
From: Kasper Daniel Hansen [mailto:kasperdanielhansen at gmail.com] 
Sent: Tuesday, January 18, 2011 5:34 PM
To: Lana Schaffer
Cc: bioconductor at r-project.org
Subject: Re: [BioC] FC calculation in Limma

What is wrong with this?  Many papers have shown that (some) noise is
additive on the log scale, so the relevant calculation should be
  ave(log(X))
Indeed, using log(ave(X)) goes against essentially the entire field of
microarray analysis.  Of course, there might be special cases, but it
seems you are making a general compliant.  So you need to come with
some convincing references to convince me (us) that there is merit in
your statement.

(of course, I am not a limma author, so my opinion caries little weight).

Kasper

Postdoc, Department of Biostatistics, Johns Hopkins University

On Tue, Jan 18, 2011 at 7:19 PM, Lana Schaffer <schaffer at scripps.edu> wrote:
> Unfortunately, we have become aware recently that the FC calculation in Limma
> Is not correct.  We input the expression values as log2 transformed values.  The
> Average log expression value is then calculated by averaging the log values (ave(logX)).
> However, this is NOT the log of the average expression value (logXbar) and so the reported
> FC is therefore not correct.
> Is there a possibility that the code can be corrected?
>
> Lana Schaffer
> Biostatistics, Informatics
> DNA Array Core Facility
> 858-784-2263
>
>
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