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

[Wolfgang Huber]

Dear Min Wook Kim,

> 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.


I am not aware of any such picture, but please have a look at the
definitions of the classes "eSet", "ExpressionSet" and "AffyBatch":

https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase/R/DataClasses.R
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/affy/R/AffyBatch.R

user: readonly
pass: readonly

Best wishes
 Wolfgang

------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


> 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"