[BioC] Affymetrix HG U295 support in BioC?

[Sole Acha, Xavi]

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
>  >>
>  >> _______________________________________________ Bioconductor mailing
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