[BioC] how to convert a AffyBatch into ExpressionSet object ?
Jenny Drnevich
drnevich at uiuc.edu
Thu Aug 23 17:02:09 CEST 2007
>
> > 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")
Be aware that you won't be able to use Excel to look at probe-level
data because Excel maxes out at ~65,000 rows (unless they've changed
something recently).
> > 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")
>
There are also functions you can use to just do background correction
or normalization without summarization, if you want to see what
effect they have. See ?bg.adjust.gcrma for gc-based background
correction, ?bg.correct for other bg correction methods, and
?normalize.methods for normalization options. expresso() is nice in
that it lets you mix-and-match between a variety of different bg
corrections, normalizations and summarization methods, and rma() and
gcrma() have arguments to turn off the background correction and/or
normalization.
Cheers,
Jenny
>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
> >>
> >>
> >
> > _______________________________________________
> > 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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