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

[Marc Carlson]

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
> >>
> >>  
> >
>