[BioC] CEL files of ALL data set

Joern Toedling toedling at ebi.ac.uk
Thu Oct 2 18:20:04 CEST 2008

Hi Willem,

I had created an R-Package containing the CEL files from those two
studies. You can retrieve it from our local repository. Within R call
repUrl <- contrib.url("http://www.ebi.ac.uk/huber-srv/data/Rrepos")
install.packages("ALLcelfiles", contriburl=repUrl)

Let me know if you encounter any problems with this. The vignette of the
package is quite basic, but at least mentions how to compare the raw
AffyBatch object with the preprocessed ExpressionSet in the ALL package.
In the long run, I guess this package should rather be added to the
Bioconductor experiment data section, but with the new release coming
up, maybe now is not the best time for that.

Best regards,

Talloen, Willem [PRDBE] wrote:
> Hi,
> I would like to do some probe-level analysis on a widely used Affymetrix data set.
> The most logical choice is the ALL data set (Chiaretti et al 2004, 2005), but I cannot find the CEL files on Arrayexpress or GEO.
> Can anybody help me with this?
> Thanks in advance,
> Willem
> [[From a mail from 2007-11-02 16:56:42 GMT on the BioC list;
>> Note that the package ALL only contains the RMA-preprocessed data. There may be a second data package containing the >raw CEL files of this data set soon. ]]
Joern Toedling
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom
Phone  +44(0)1223 492566
Email  toedling at ebi.ac.uk

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