'Re: [BioC] Affymetrix HG U295 support in BioC?'

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List:       bioconductor
Subject:    Re: [BioC] Affymetrix HG U295 support in BioC?
From:       cstrato <cstrato () aon ! at>
Date:       2010-06-29 15:52:28
Message-ID: 4C2A16BC.4000406 () aon ! at
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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@aon.at]
> Enviado el: lunes, 28 de junio de 2010 21:16
> Para: Sole Acha, Xavi
> CC: James W. MacDonald; bioconductor@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@aon.at]
> > Enviado el: lun 28/06/2010 20:11
> > Para: Sole Acha, Xavi
> > CC: James W. MacDonald; bioconductor@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@med.umich.edu]
> > > Enviado el: lunes, 28 de junio de 2010 18:18
> > > Para: Sole Acha, Xavi
> > > CC: bioconductor@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
> > > > list Bioconductor@stat.math.ethz.ch
> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the
> > > > archives:
> > > > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > > 
> > 
> > 
> 

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