[BioC] RMA question

[F Duan]

Something like "rma(data, background = MAS, normalize = FALSE)"
will work for you.

Actually, there are a lot of options for users to choose.

good luck.

Frank

Quoting Fangxin Hong <fhong at salk.edu>:

> 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
> >
> >
> >
> >
> > 	[[alternative HTML version deleted]]
> >
> > _______________________________________________
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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
> 
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