[BioC] Example on constructing AffyBatch object

[James W. MacDonald]

Look at the code for read.affybatch.

Best,

Jim



On 7/1/2010 12:29 PM, Peng Yu wrote:
> Hi,
>
> I see that I can use data() to load AffyBatch object from affydata, or
> I could load cel files to get AffyBatch. But I'd rather construct an
> example AffyBatch object using fake data so that I can understand how
> AffyBatch works.
>
> I adapted the example from Biobase (note that I don't load any data
> from a file) which help me understand exactly the member functions and
> the object construction. But I don't find such a tutorial for
> AffyBatch. If it is available somewhere, would you please point it me.
> If it is not, would give some examples so that I can understand how
> AffyBatch is constructed and how the new member functions in AffyBatch
> (as AffyBatch is inherent from ExpressionSet) is related to the
> construction?
>
> library('Biobase')
> nFeatures=10
> nSamples=4
> exprs=matrix(runif(nFeatures*nSamples), nrow=nFeatures, ncol=nSamples)
> colnames(exprs)=LETTERS[1:nSamples]
> rownames(exprs)=letters[1:nFeatures]
>
> set.seed(0)
>
> varlabels=c('gender', 'type')
> pData=data.frame(
>      sample(c('Female', 'Male'), nSamples, replace=T)
>      , sample(c('Control', 'Case'), nSamples, replace=T)
>      )
> names(pData)=varlabels
> row.names(pData)=LETTERS[1:nSamples]
>
> metadata=data.frame(
>      labelDescription=c('Patient gender', 'Case/control status')
>      , row.names=varlabels
>      )
>
> pData
> metadata
>
> phenoData=new('AnnotatedDataFrame', data=pData, varMetadata=metadata)
> str(phenoData)
>
> experimentData=new(
>      'MIAME',
>      name='Pierre Fermat',
>      lab='Francis Galton Lab',
>      contact='pfermat at lab.not.exist',
>      title='Smoking-Cancer Experiment',
>      abstract='An example ExpressionSet',
>      url='www.lab.not.exist',
>      other=list(notes='Created from text files')
>      )
>
> annotation='hgu95av2'
>
> eset=new('ExpressionSet', exprs=exprs, phenoData=phenoData,
> experimentData=experimentData, annotation=annotation)
>
> exprs(eset)
> featureNames(eset)
> sampleNames(eset)
> phenoData(eset)
> experimentData(eset)
>
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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