[R] RMA question

Adaikalavan Ramasamy ramasamy at cancer.org.uk
Thu Oct 21 22:57:31 CEST 2004

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 
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