[BioC] RMA question

[Fangxin Hong]

There are some alternatives to do background correction and  normalization
separately, and you can specify he methods you want to us.

like
data.bg<-bg.correct.mas(data)
data.bg.nor<-normalize.AffyBatch.quantiles(data.bg, type="together")

Fx

> Can anybody explain why RMA has a default normalization method:
> quantile-quantile?  Why don't leave the choices to users?
>
>
>
> If I just want to run RMA for a background correction without
> normalization,
> how should I specify the in the expresso function, in
> the other word, normalize.method="?"
>
>
>
> Hairong
>
>
>
>
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-- 
Fangxin Hong, Ph.D.
Plant Biology Laboratory
The Salk Institute
10010 N. Torrey Pines Rd.
La Jolla, CA 92037
E-mail: fhong at salk.edu