[BioC] Affymetrix HT HG-U133+ PM Array Plate annotation data

[giacomo.tuana at unimib.it]

   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
   >>
   >>
   >