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

[Jenny Drnevich]

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