Dear list, I found only cdf and probe packages for Affymetrix HT HG-U133+ PM Array Plate but there isn't the annotation data package (hthgu133pluspm.db) in Bioc 2.5 and in developing Bioc 2.6. It could be released soon? Thanks! Giacomo Tuana -- Dr. Giacomo Tuana Franguel Genopolis Consortium University of Milano-Bicocca Dept. of Biotechnology and Bioscience/ U4 Piazza della Scienza 4 20126 Milano, Italy http://www.genopolis.it

Hi Giacomo, We don't presently have an annotation package for that platform. But fortunately, we have a solution for you. You can use the SQLForge code in the AnnotationDbi package to just generate a package from an the Affy probe to gene mapping files (which you can get from their website). There is a vignette explaining how to do this here: http://www.bioconductor.org/packages/2.6/bioc/html/AnnotationDbi.html Please let me know if you have any trouble. Marc giacomo.tuana at unimib.it wrote: > Dear list, > I found only cdf and probe packages for Affymetrix HT HG-U133+ PM Array > Plate but there isn't the annotation data package (hthgu133pluspm.db) in > Bioc 2.5 and in developing Bioc 2.6. It could be released soon? > Thanks! > Giacomo Tuana > -- > Dr. Giacomo Tuana Franguel > Genopolis Consortium > University of Milano-Bicocca > Dept. of Biotechnology and Bioscience/ U4 > Piazza della Scienza 4 20126 Milano, Italy > http://www.genopolis.it > _______________________________________________ > 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 > >

Dear Giacomo, You can use the package "xps" which supports all plate arrays and uses the Affymetrix annotation files for the plate 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 _._._._._._._._._._._._._._._._._._ giacomo.tuana at unimib.it wrote: > Dear list, > I found only cdf and probe packages for Affymetrix HT HG-U133+ PM Array > Plate but there isn't the annotation data package (hthgu133pluspm.db) in > Bioc 2.5 and in developing Bioc 2.6. It could be released soon? > Thanks! > Giacomo Tuana > -- > Dr. Giacomo Tuana Franguel > Genopolis Consortium > University of Milano-Bicocca > Dept. of Biotechnology and Bioscience/ U4 > Piazza della Scienza 4 20126 Milano, Italy > http://www.genopolis.it > _______________________________________________ > 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 > >

Hi Giacomo, The call to system.file() is just inserted into the example so that this example will always be able to find an example file independent of where your R library is located. The value for "hcg110_ID" can therefore be replaced with a simple string containing the path to your probeIDs file. Please note that the probeIDs file itself must be tab delimited and free of headers. Marc giacomo.tuana at unimib.it wrote: > Dear Marc, > > I had some trouble with reading external file of probeIDs. I didn't > understand completely the use of system.file( ) command. In the > tutorial I found: > system.file ("extdata", "hcg110_ID",package="AnnotationDbi") > where "extdata" should be my personal tab delimited file for probe ids > and hcg110_ID the source database file? > I'm sorry, but this is the first time I use this commands. > > Giacomo > > > -- > > Dr. Giacomo Tuana Franguel > > Genopolis Consortium > University of Milano-Bicocca > Dept. of Biotechnology and Bioscience/ U4 > Piazza della Scienza 4 20126 Milano, Italy > Tel +39 02 6448 3530 > Fax +39 02 6448 3550 > http://www.genopolis.it > > > > On Fri, 18 Dec 2009 10:00:08 -0800 > Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > > Hi Giacomo, > > > > We don't presently have an annotation package for that > >platform. But > > fortunately, we have a solution for you. You can use > >the SQLForge code > > in the AnnotationDbi package to just generate a package > >from an the Affy > > probe to gene mapping files (which you can get from > >their website). > > There is a vignette explaining how to do this here: > > > > http://www.bioconductor.org/packages/2.6/bioc/html/AnnotationDbi.html > > > > Please let me know if you have any trouble. > > > > > > Marc > > > > > > > > > > giacomo.tuana at unimib.it wrote: > >> Dear list, > >> I found only cdf and probe packages for Affymetrix HT > >>HG-U133+ PM Array > >> Plate but there isn't the annotation data package > >>(hthgu133pluspm.db) in > >> Bioc 2.5 and in developing Bioc 2.6. It could be > >>released soon? > >> Thanks! > >> Giacomo Tuana > >> -- > >> Dr. Giacomo Tuana Franguel > >> Genopolis Consortium > >> University of Milano-Bicocca > >> Dept. of Biotechnology and Bioscience/ U4 > >> Piazza della Scienza 4 20126 Milano, Italy > >> http://www.genopolis.it > >> _______________________________________________ > >> 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 > >> > >> > > >