[BioC] Affymetrix HG U295 support in BioC?

[cstrato]

Dear Xavier,

Your version of xps is much too old, I would suggest to upgrade to the 
current version xps_1.8.1. In any case you can find example 7 when you 
download the source of the newest version.

Best regards
Christian

On 6/29/10 11:52 AM, Sole Acha, Xavi wrote:
> Dear Chris,
>
> I can't find such "example 7" in the file you mention, neither also in the other files in the "examples" folder. I'm using xps 1.4.10. Maybe it is located somewhere else?
>
> Thanks!
>
> Xavi.
>
>
> -----Mensaje original-----
> De: cstrato [mailto:cstrato at aon.at]
> Enviado el: lunes, 28 de junio de 2010 21:16
> Para: Sole Acha, Xavi
> CC: James W. MacDonald; bioconductor at stat.math.ethz.ch; Cordero Romera, David
> Asunto: Re: [BioC] Affymetrix HG U295 support in BioC?
>
> Dear Xavier,
>
> Actually, example 7 of script "script4xps.R", located in xps/examples,
> shows you how to import the 6 sample CEL files from Affymetrix.
>
> Best regards
> Christian
>
>
> On 6/28/10 9:05 PM, Sole Acha, Xavi wrote:
>> Dear Christian,
>>
>> thank you for your help. I will have a look at your package for sure.
>> Actually, we already have it installed on our servers (along with root),
>> and will try it with the 6 sample CEL files provided by Affy's website
>> (I'm still waiting for our own data).
>>
>> Thank you so much!
>>
>> Xavi.
>>
>>
>> -----Mensaje original-----
>> De: cstrato [mailto:cstrato at aon.at]
>> Enviado el: lun 28/06/2010 20:11
>> Para: Sole Acha, Xavi
>> CC: James W. MacDonald; bioconductor at stat.math.ethz.ch
>> Asunto: Re: [BioC] Affymetrix HG U295 support in BioC?
>>
>> 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
>> Christian
>> _._._._._._._._._._._._._._._._._._
>> 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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>>
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