[BioC] Affymetrix HG U295 support in BioC?
cstrato at aon.at
Tue Jun 29 17:52:28 CEST 2010
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.
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?
> -----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
> 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!
>> -----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
>> 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
>> >> _______________________________________________ Bioconductor mailing
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