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 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 Sol? Acha Unitat de Biomarcadors i Susceptibilitat Unit >> >> of Biomarkers and Susceptibility Institut Catal? 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 at stat.math.ethz.ch >> >> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the >> >> archives: >> >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > >> >> >