[BioC] Affymetrix HG U295 support in BioC?

[cstrato]

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
>  >>
>  >> _______________________________________________ Bioconductor mailing
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>
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