Thank Rafa for answering the question. From the response of Earl Hubbell to
my email, this is one of the operations to stabilize variance on the
log-scale in order to match the assumption used in the tests of Affycomp
site (i.e., stable variance). More topics about variance stabilization are
covered in this reference:
http://bioinformatics.oxfordjournals.org/cgi/screenpdf/19/8/966.

Thanks,

Frank

On 3/6/06, Rafael A. Irizarry <ririzarr@jhsph.edu> wrote:
>
> to avoid dividing by numbers close to 0. earl added 16 to the
> PLIER expression values (before log!) and 32 to the MAS 5.0 ones.
>
>
> On Mon, 6 Mar 2006, James W. MacDonald wrote:
>
> > Frank Duan wrote:
> >> Hi All,
> >>
> >> Sorry to raise up this question again. I did search the forum but
> failed to
> >> get the answer.
> >>
> >> Can anyone has an idea what "16" means in "plier+16"?
> >
> > Why don't you email Earl Hubbell directly and ask him? You can get his
> > email off the affycomp website.
> >
> > Best,
> >
> > Jim
> >
> >
> >
> > --
> > James W. MacDonald, M.S.
> > Biostatistician
> > Affymetrix and cDNA Microarray Core
> > University of Michigan Cancer Center
> > 1500 E. Medical Center Drive
> > 7410 CCGC
> > Ann Arbor MI 48109
> > 734-647-5623
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >
>

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