[BioC] Expressionset from ArrayExpress processed data

[Misha Kapushesky]

Hi,

Audrey (the author of the ArrayExpress package) will probably be able  
to give a more precise answer, but I believe a capacity for the this  
package to return ExpressionSet objects from processed data in AE is  
planned and such an implementation may be available in the development  
branch (check bioc svn). Audrey?

--Misha
On 20 Jan 2009, at 14:26, Martin Morgan wrote:

> 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
>
>  http://bioconductor.org/packages/2.3/bioc/html/Biobase.html
>
> 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)
>
> Martin
>
>> 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
>> Abreu" de Las Villas Carretera a Camajuaní km 5½, Santa Clara, Villa
>> Clara, Cuba Tel: 53 (42) 281257, 281268, 281693 Fax: 53 (42) 281329
>> Web: http://www.ibp.co.cu E-Mail: info at ibp.co.cu
>>
>> _______________________________________________ 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
>
> -- 
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M2 B169
> Phone: (206) 667-2793
>
> _______________________________________________
> 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