[BioC] Expressionset from ArrayExpress processed data

Martin Morgan mtmorgan at fhcrc.org
Tue Jan 20 15:26:19 CET 2009

Hi Yovanny

Yovanny Izquierdo Núñez <yovanny at ibp.co.cu> writes:

> Dear BioC users,
> I'm working with experiments from the ArrayExpress database and some
> of them do not provide the cell files, but instead the already
> processed data in a table fromat (esasy to read with read.delim, for
> instance). The PhenoData of the experiment comes separately in the
> sdrf file. Is there a way to create an expressionset object from these
> two?  The ArrayExpress package only provides functions for creating an

See the 'ExpressionSetIntroduction.pdf' in the Biobase package


I don't know how to parse the PhenoData into a data.frame, but once
done likely you'll be able to do

  phenoData <- new("AnnotatedDataFrame", pData=PhenoData)
  eset <- new("ExpressionSet", exprs=exprs, phenoData==phenoData)


> AffyBatch object from the raw data and the sdrf, adf and idf files;
> but has nothing so far to deal with the processed data.
> Thanks so much,
> Yovanny
> Instituto de Biotecnología de las Plantas Universidad Central "Marta
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> Clara, Cuba Tel: 53 (42) 281257, 281268, 281693 Fax: 53 (42) 281329
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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