[BioC] Affymetrix HG U295 support in BioC?

cstrato cstrato at aon.at
Mon Jun 28 20:11:14 CEST 2010

Dear Xavier,

Alternatively, you could use package xps, which also supports the 
HG-U219 arrays. It uses the official CDF and annotation files from 
Affymetrix to create so-called "root scheme files". However, you can 
download the pre-built scheme file "hgu219_na30.root" from:

Besides rma normalization xps also allows you to do mas5 normalization 
for PM-only arrays.

Best regards
C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

On 6/28/10 7:19 PM, Sole Acha, Xavi wrote:
> 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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