[BioC] VSN combined with RMA

[Rafael Irizarry]

in principle it does not sound like a good idea since vsn does  
something that could be considered bg correction.

in any case i have already seen the result of this and you get very  
similar results to just using RMA (quantile normalization). look at the  
RMAVSN entry in
http://affycomp.biostat.jhsph.edu





On Jul 19, 2004, at 3:56 PM, Remo Sanges wrote:

> I' m planning to test vsn normalization on affymetrix arrays
> with RMA background correction.
>
> But from the vsn vignette and other messages in this list
> it seems to me that vsn on affymetrix chips is used without
> background correction:
> e=expresso(data,bg.correct=FALSE,normalize.method="vsn",pmcorrect.metho 
> d="pmonly",summary.method="medianpolish")
>
> There is a reason for this?
>
> Is it wrong to use expresso in this way:
> e=expresso(data,bg.correct="rma",normalize.method="vsn",pmcorrect.metho 
> d="pmonly",summary.method="medianpolish") ?
>
> Thank you
>
> Remo
>
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