[BioC] Affymetrix HG U295 support in BioC?
cstrato at aon.at
Mon Jun 28 21:16:24 CEST 2010
Actually, example 7 of script "script4xps.R", located in xps/examples,
shows you how to import the 6 sample CEL files from Affymetrix.
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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