[BioC] Question about MAS5 implementation in Affy package

[Rafael A. Irizarry]

On Fri, 16 May 2003 Dapeng.Xu at aventis.com wrote:

> Here is what I run:
> 
> > Data <- ReadAffy()
> > eset <- expresso(Data, normalize=FALSE,
> bgcorrect.method="mas",pmcorrect.method="mas",summary.method="mas")
> 
> 
> The method "mas" should be MAS5 method as it says in the introduction
> document.

the code was written using mas a short-hand for MAS 5.0. 

> 
> But the output file only has 2 columns: qualifier names and numerical signal
> values. 
> 
> How do I get absent/present decision calls?

expresso returns expression values not present absent calls. 
present/absent calls, as implemented by Affymetrix is 
not currently implemeneted. however, its relatively easy to code if you 
have the MAS 5.0 manual. 

> 
> Dapeng
> 
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