[BioC] Affymetrix HG U295 support in BioC?

James W. MacDonald jmacdon at med.umich.edu
Mon Jun 28 18:17:57 CEST 2010

Hi Xavier,

Sole Acha, Xavi wrote:
> Dear listers,
> I would be pleased if someone could tell me if there are any plans to
> include the new Affymetrix HG U295 arrays in the list of supported
> platforms for "standard" affy analysis packages (affy,
> simpleaffy,...). Although the array came out a few months ago, it
> seems that the CDF has not been included in the BioC release yet. By
> now, the only BioC package I've found that seems to support these new
> array plates is xps. Does someone know anything more about this?

I don't see a HG-U295 chip on the Affy website, but I do see a HG-U219. 
Is that a typo on your part?

If not, can you give a link to the correct webpage?

I have built cdf and probe packages for the HG-U219 chip, but note that 
these will only work with the affy and affyPLM packages. Since the chips 
are PM-only, they won't work with simpleaffy, and will require some work 
on your part to get to work with gcrma, if at all.



> Thank you very much for your help in advance.
> Best regards,
> ------ Xavier Solé Acha Unitat de Biomarcadors i Susceptibilitat Unit
> of Biomarkers and Susceptibility Institut Català d'Oncologia //
> Catalan Institute of Oncology Gran Via de L'Hospitalet 199-203 08907
> L'Hospitalet de Llobregat, Barcelona, Spain. Phone: +34 93 260 71 86
> / +34 93 335 90 11 (ext. 3194) Fax: +34 93 260 71 88 E-mail: x.sole
> (at) iconcologia.net
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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