[BioC] multiple Affy normalization results in single object ?

[Martin Morgan]

Hi Wolfgang --

Wolfgang Raffelsberger wrote:
> Dear list,
> 
> I'm wondering if / how I could store the results from multiple multiple
> Affy summarization/normalization approaches (eg RMA, vsn, etc) in a
> single object.
> Does the Biobase ExpressionSet support this ( I haven't succeded in
> doing so) or do I have to create a now class of objects ?
> 
> Of course the simples way would be something like :
> require(affy);  require(vsn)
> eset <- ReadAffy()
> combExps <- list(rma=exprs(rma(eset)),vsn= exprs(vsnrma(eset.cel))    #
> and so on for more methods...
> 
> I suppose other people have already thought about this and I wonder if
> there are more elegant solutions like the code above...

ExpressionSet assayData must have an 'exprs' matrix, but can also have
others, added by assayDataElement<-. So

abatch <- ReadAffy()
combo = rma(abatch)
assayDataElement(combo, "vsn") = vsnrma(abatch)

and so on. Then things like

combo[,1:10]

do a coordinate subset. Retrieve the data with assayData(combo)[["vsn"]]

Martin

> 
> For completeness :
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> i386-pc-mingw32
> 
> locale:
> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252
> 
> 
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base   
> other attached packages:
> [1] MASS_7.2-47          fdrtool_1.2.5        limma_2.18.2        
> affyPLM_1.20.0       preprocessCore_1.6.0 gcrma_2.16.0        
> Biostrings_2.12.7  [8] IRanges_1.2.3        affy_1.22.0         
> Biobase_2.4.1     
> loaded via a namespace (and not attached):
> [1] affyio_1.12.0 splines_2.9.1 tools_2.9.1
> Thank's in advance,
> Wolfgang
> 
> 
> . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
> Wolfgang Raffelsberger, PhD
> Laboratoire de BioInformatique et Génomique Intégratives
> CNRS UMR7104, IGBMC,  1 rue Laurent Fries,  67404 Illkirch  Strasbourg, 
> France
> Tel (+33) 388 65 3300         Fax (+33) 388 65 3276
> wolfgang.raffelsberger (a t) igbmc.fr
> 
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