multiple Affy normalization results in single object ?
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@wolfgang-raffelsberger-2876
Last seen 11 months ago
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 G?nomique Int?gratives 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
Biobase vsn Biobase vsn • 521 views
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@martin-morgan-1513
Last seen 22 days ago
United States
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_MONETAR Y=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 G?nomique Int?gratives > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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