[BioC] About between-array normalization in limma

[Ramon Diaz-Uriarte]

Dear Simon,

On Wednesday 24 October 2007 02:32, Simon Lin wrote:
> Sean Davis Wrote:
> >The rule-of-thumb is that if you are working with two-color data and
> >using ratios only, then you probably do not need between-array
> >normalization.
>
> What is the rationale behind this claim? Is it because the common ref
> channel serves as kind of internal calibration control already?
>

I think (at least part of) the argument had to do with the variance-bias 
trade-off. And I think the NAR paper by Dudoit et al. on normalization had 
some comments regarding these issues (though that paper is a few years old by 
now). I think I also remember seening a pdf of a talk by K. Kerr and 
colleagues where these issues might have been addressed (though I am not 
sure).

Anyway, I'm also interested in knowing if there are stronger arguments and 
more recent studies.

Best,

R.

> Seems that the current recommendation of normalization is on the less
> agreesive side?
>
> -Simon
>
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-- 
Ramón Díaz-Uriarte
Statistical Computing Team
Centro Nacional de Investigaciones Oncológicas (CNIO)
(Spanish National Cancer Center)
Melchor Fernández Almagro, 3
28029 Madrid (Spain)
Fax: +-34-91-224-6972
Phone: +-34-91-224-6900

http://ligarto.org/rdiaz
PGP KeyID: 0xE89B3462
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