[BioC] RMA vs VSN

[Rafael A. Irizarry]

vsn and rma are not competitors. the first is a normalization
technique, the second is a way to obtain expression measures from affy
arrays which includes background adjustment, normaliztion, and
summarization. rma uses quantile normalization as a default.
changing this to vsn yields, in general, very similar results. 

notice, some use rma to obtain an expression measure and then
use vsn to nromalize that, although i worry this could result in
over-normalization.

On Sat, 19 Jun 2004, Roger Vallejo wrote:

> We have a small experiment with high FDR (around 0.40): 8 affymetrix
> mouse genechips with 22k genes, 2 replications, saline and E. coli
> treated mammary tissue, evaluated at 24 hr and 48 hr post injections. 
> 
> I have run both data preprocessing functions via expresso. To
> subsequenctly run an lme-ANOVA.  As expected, I got lower FDR and much
> smaller p-values when using VSN. The FDR was estimated using QVALUE
> package. Obviously, I feel tempted to use VSN instead of RMA. However,
> before proceeding I would like to hear some comments from the
> Bioconductor group on this approach. The question is:
> 
> Is VSN better than RMA? 
> 
> I have read the literature and both claim to be the function to be used!
> 
> 
> Personally, I feel more towards the use of VSN. I might be wrong, so I
> would appreciate any suggestions or comments on this. 
> 
> These are the functions that I used:
> 
> *************************************************************
> 
> For RMA:
> 
> > library(affy)
> 
> > Data <- ReadAffy(widget=TRUE)
> 
> 
> > eset <- expresso(Data,bgcorrect.method="rma",
> normalize.method="quantiles", pmcorrect.method="pmonly",
> summary.method="medianpolish")
> 
>  
> 
> ********************************************************************
> 
> For VSN:
> 
> > library(affy)
> 
> > Data <- ReadAffy(widget=TRUE)                                         
> 
> > library(vsn)
> 
> > normalize.AffyBatch.methods <- c(normalize.AffyBatch.methods, "vsn")
> 
> > eset = expresso(Data, bg.correct= FALSE, normalize.method = "vsn",
> pmcorrect.method = "pmonly", summary.method = "medianpolish")
> 
>  
> 
> ************************************************************************
> ************************************
> 
> Thank you very much.
> 
> Roger
> 
>  
> 
>  
> 
> Roger L. Vallejo, Ph.D.
> 
> Assist. Professor of Genomics & Bioinformatics
> 
> Genomics & Bioinformatics Laboratory
> 
> Department of Dairy & Animal Science
> 
> The Pennsylvania State University
> 
> 305 Henning Building
> 
> University Park, PA 16802
> 
> Phone:       (814) 865-1846 
> 
> Email:        rvallejo at psu.edu
> 
>  
> 
> 
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> 
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