[BioC] Expressionset from ArrayExpress processed data

[audrey at ebi.ac.uk]

Hi all,

I do not especially want to encourage everyone to use the development
version of the package as I am still working on it and it is unstable.
But, you can still try to use the version 1.3.6 of the
package ArrayExpress. This version does offer functions for processed
data (using getAE then getcolproc and then procset, see procset help).
However; if there is a problem of mapping between the sdrf file and the
expression files, the phenoData will not be created using the ArrayExpress
package. This is a very specific situation and I do not think there is a
good automated way to handle it without taking the risk of doing something
wrong.

I will be happy to have your feedback on these functions.

Cheers,
Audrey

> 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
>>>
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>>
>> --
>> 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
>>
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>
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