[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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