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

Thu Aug 23 13:45:03 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.

Min Wook,

To my knowledge, unfortunately there is not any such picture.
Having a diagram of the classes would be good idea indeed
(as it would point developers quickly to existing classes and
their relationships)... and may be a also a good exercise
to build it automatically from R using introspection and Rgraphviz.

> 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.

What about the following ?
write.csv(exprs(abatch), file="myProbeLevelData.csv")

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

Did you try this ?
help("expresso", package="affy")

Hoping this helps,

Laurent

> 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"
>> >
>> >_______________________________________________
>> >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
>>
>> 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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