[BioC] Affymetrix HG U295 support in BioC?

[Sole Acha, Xavi]

Hi Jim,

Sorry... that was a mistake of mine. Certainly I was talking about U219 arrays.

Are the cdf files you've built available? That would be of great help to me.

Besides that... I guess there is a kind of mas5-like normalization for PM-only arrays... maybe newer versions of BioC may handle it.

Thank you very much for your help.

Xavi.



-----Mensaje original-----
De: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Enviado el: lunes, 28 de junio de 2010 18:18
Para: Sole Acha, Xavi
CC: bioconductor at stat.math.ethz.ch
Asunto: Re: [BioC] Affymetrix HG U295 support in BioC?

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.

Best,

Jim


> 
> 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.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
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734-615-7826
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