[BioC] how to convert a AffyBatch into ExpressionSet object ?

Min Wook Kim labohemekim at gmail.com
Thu Aug 23 11:01:52 CEST 2007


Hi Jenny,
thanks a lot. I know the relationship between AffyBatch and
ExpressionSet. but I wanted to find some pictures about the classes
hierarchy for more readable and understandable one.

and, why I converted the probe-level data into the probeset data was
that I wanted to compare those data by looking directly in excel file.
but I can't find how to write the excel file from probe-leve data of
the AffyBatch Object. so I tried to do it.

and I wanted that it was possible to copy or convert from affybatch
object to expression data with some modification directly but without
normalization.

sincerely
Minwook

On 8/22/07, Jenny Drnevich <drnevich at uiuc.edu> wrote:
> Hi Min Wook,
>
> The discrepancy is because you are comparing the probe-level data
> from an AffyBatch object to the probeset-level data of an
> ExpressionSet created by gcrma().  Why would you want to convert an
> AffyBatch object directly into an ExpressionSet object without
> summarizing the probe-level data into probeset data? The AffyBatch
> object extends the ExpressionSet structure specifically for
> probe-level data (individual PM and MM intensities), and typically
> ExpressionSet objects are reserved for summarized probeset data. For
> more details on the data classes, use ?"AffyBatch" and ?"ExpressionSet".
>
> Cheers,
> Jenny
>
> At 11:42 AM 8/22/2007, Min Wook Kim wrote:
> >Dear all,
> >I tried to convert a object of AffyBatch into one of ExpressionSet.
> >but I couldn't get exactly same information between them, actually,
> >The data between original data and the modified data from gcrma was
> >compared.
> >
> >The problem was that the assayData and fetureaData didn't match. Do I
> >have to make new object of AssayData and featuredata by using "new
> >command" ? are there any easy way ? e.g. some function to copy from
> >one to the other.
> >
> >I did it like ;
> > > abatch
> >AffyBatch object
> >size of arrays=1002x1002 features (8 kb)
> >cdf=Mouse430_2 (45101 affyids)
> >number of samples=4
> >number of genes=45101
> >annotation=mouse4302
> >notes=
> > > tmp <- new ("ExpressionSet", phenoData = phenoData(abatch) ,
> > featureData = featureData(abatch), experimentData =
> > experimentData(abatch), annotation =
> > annotation(abatch),  assayData= assayData(abatch))
> >
> >
> >And what's difference between the following statement and above which
> >were different in assayData defined and exprs )
> >
> > > tmp <- new ("ExpressionSet", phenoData = phenoData(abatch) ,
> > featureData = featureData(abatch), experimentData =
> > experimentData(abatch), annotation = annotation(abatch),   exprs =
> > exprs(abatch) )
> >
> >-------------------------------------------
> >Finally, I want to make the same structure of the following two
> >objects except the value depending on the effect of gcrma. myRMA was
> >the output of gcrma. Maybe, my trying has a big misunderstanding of
> >them. if do it, please tell me it.
> >
> >
> > > myRMA
> >ExpressionSet (storageMode: lockedEnvironment)
> >assayData: 14707 features, 4 samples
> >   element names: exprs
> >phenoData
> >   sampleNames: HM1_24, HM1_25, Flt3_a, Flt3_b
> >   varLabels and varMetadata:
> >     sample: arbitrary numbering
> >     pheno1: arbitrary numbering
> >featureData
> >   rowNames: 1415670_at, 1415671_at, ..., AFFX-TransRecMur/X57349_3_at
> >(14707 total)
> >   varLabels and varMetadata: none
> >experimentData: use 'experimentData(object)'
> >Annotation [1] "mouse4302"
> > > tmp
> >ExpressionSet (storageMode: lockedEnvironment)
> >assayData: 1004004 features, 4 samples
> >   element names: exprs
> >phenoData
> >   sampleNames: HM1_24, HM1_25, Flt3_a, Flt3_b
> >   varLabels and varMetadata:
> >     sample: arbitrary numbering
> >     pheno1: arbitrary numbering
> >featureData
> >   featureNames: 1, 2, ..., 1004004 (1004004 total)
> >   varLabels and varMetadata: none
> >experimentData: use 'experimentData(object)'
> >Annotation [1] "mouse4302"
> >--------------------------------------------------------------------
> >
> >And additionally, I haven't been able find the picture of description
> >about the hierarchy of classes ; especially Affybatch , EspressionSet
> >and eSet. If to exist, it would be so helpful.
> >
> >
> >
> >
> > > sessionInfo()
> >R version 2.5.1 (2007-06-27)
> >powerpc64-unknown-linux-gnu
> >
> >locale:
> >LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
> >
> >attached base packages:
> >   [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "datasets"
> >   [7] "tcltk"     "utils"     "methods"   "base"
> >
> >other attached packages:
> >mouse4302cdf          vsn       marray    tkWidgets      GOstats     Category
> >     "1.16.0"      "2.2.0"     "1.14.0"     "1.14.0"      "2.2.6"      "2.2.3"
> >       Matrix         RBGL        graph     multtest      annaffy         KEGG
> >"0.999375-1"     "1.12.0"     "1.14.2"     "1.16.1"      "1.8.1"     "1.16.1"
> >           GO        limma affyQCReport  geneplotter      lattice     annotate
> >     "1.16.0"     "2.10.5"     "1.14.0"     "1.14.0"    "0.15-11"     "1.14.1"
> >RColorBrewer      affyPLM        gcrma  matchprobes     affydata       xtable
> >      "1.0-1"     "1.12.0"      "2.8.1"      "1.8.1"     "1.11.3"      "1.5-1"
> >   simpleaffy   genefilter     survival         affy       affyio      Biobase
> >    "2.10.31"     "1.14.1"       "2.32"     "1.14.2"      "1.4.1"     "1.14.1"
> >       DynDoc  widgetTools
> >     "1.14.0"     "1.12.0"
> >
> >_______________________________________________
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>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich at uiuc.edu
>
>



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