[BioC] multiple Affy normalization results in single object ?

Wolfgang Raffelsberger wraff at igbmc.fr
Fri Sep 4 12:40:54 CEST 2009


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...

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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