[BioC] limma - RG.MA

[Naomi Altman]

Yes, I forgot the factor of 2.  Sorry to keep making these silly mistakes.

--Naomi

At 06:44 AM 12/17/2005, Gordon K Smyth wrote:
> > Date: Fri, 16 Dec 2005 21:06:57 -0500
> > From: Naomi Altman <naomi at stat.psu.edu>
> > Subject: [BioC] limma - RG.MA
> > To: bioconductor at stat.math.ethz.ch
> >
> > Shouldn't RG.MA be:
> >
> > function (object)
> > {
> >      object$R <- 2^((object$A + object$M)/2)
> >      object$G <- 2^((object$A - object$M)/2)
> >      object$M <- NULL
> >      object$A <- NULL
> >      new("RGList", unclass(object))
> > }
> >
> > Naomi S. Altman                                814-865-3791 (voice)
> > Associate Professor
> > Dept. of Statistics                              814-863-7114 (fax)
> > Penn State University                         814-865-1348 (Statistics)
> > University Park, PA 16802-2111
>
>No, the code is correct as it is.  Don't forget that A=(logR+logG)/2 
>involves a factor of 2 in its
>definition while M=logR-logG does not.  Hence only M is divided by 2 
>in the reverse computation.
>
>Best wishes
>Gordon
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111