R help - Oct 2004 - RMA question

Can anybody explain why RMA has to have a default normalization method:
quantile-quantile?  Why don't leave the choices to users? 

If I just want to use RMA to do a background correction without
normalization, how should I specify the ? in the normalize.method="?"
?

 

Hairong 


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1. This question is more appropriate for the BioConductor mailing list.

2. Any Affymetrix pre-processing can be split into background
correction, normalisation and summary stages. The combination of rma
background, quantile normalisation and median polish summary gives rise
to RMA. Therefore quantile normalisation is a defining feature of RMA. 
( which is probably why when the authors of RMA improved the background
stage, they called it GC-RMA instead ).

3. You can certainly mix and match any stages you like using the
expresso function. See help(expresso).
 


On Thu, 2004-10-21 at 21:14, Hairong Wei wrote:
> Can anybody explain why RMA has to have a default normalization method:
> quantile-quantile?  Why don't leave the choices to users? 
> 
> If I just want to use RMA to do a background correction without
> normalization, how should I specify the ? in the
normalize.method="?" ?
> 
>  
> 
> Hairong 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>

Hairong Wei wrote:
> Can anybody explain why RMA has to have a default normalization method:
> quantile-quantile?  Why don't leave the choices to users? 
> 
> If I just want to use RMA to do a background correction without
> normalization, how should I specify the ? in the
normalize.method="?" ?
What is RMA? It's not in base R, AFAIK.
Do you mean function rma() in the Bioconductor package "affy"? In this
case please ask for help on the Bioconductor list.

Uwe Ligges

>  
> 
> Hairong 
> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html