[BioC] [R] Is there a package similar to mogene10stprobeset.dbby for Affymetrix Exon Arrays?

[Groot, Philip de]

Dear Peng,
 
There is a MBNI custom CDF package available for this chip.
 
More information is available here: 
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp
 
I maintain a page with the most up-to-date annotation libraries for many MBNI Custom CDF files (including the one you are looking for).
This includes packages for the just-released Bioconductor-2.5 version:
http://nugo-r.bioinformatics.nl/NuGO_R.html
 
Regards,
 
Dr. Philip de Groot Ph.D.
Bioinformatics Researcher

Wageningen University / TIFN
Nutrigenomics Consortium
Nutrition, Metabolism & Genomics Group
Division of Human Nutrition
PO Box 8129, 6700 EV Wageningen
Visiting Address: Erfelijkheidsleer: De Valk, Building 304
Dreijenweg 2, 6703 HA  Wageningen
Room: 0052a
T: +31-317-485786
F: +31-317-483342
E-mail:   Philip.deGroot at wur.nl <mailto:Philip.deGroot at wur.nl> 
Internet: http://www.nutrigenomicsconsortium.nl <http://www.nutrigenomicsconsortium.nl/> 
             http://humannutrition.wur.nl <http://humannutrition.wur.nl/> 
             https://madmax.bioinformatics.nl <https://madmax.bioinformatics.nl/> 
 
 
 

________________________________

From: Tony Chiang [mailto:tchiang at fhcrc.org]
Sent: Wed 28-10-2009 2:33
To: Peng Yu
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] [R] Is there a package similar to mogene10stprobeset.dbby for Affymetrix Exon Arrays?



Please don't cross post to the lists, especially for a thread that you
started on one list. This is not helpful for archiving and searching the
list for past posts.

As for what you are asking, Marc's e-mail he said you should look at the
webpage, and then if *you don't find the data package that you want,* you
can the AnnotationDbi package (particularly SQLForge) to create such a
package for yourself. You can also share it with others if you wish. There
should be documentation in the package vignette to help you create such a
package (Marc can point you to other documentation if they exist, but I
think that the vignette and man pages should suffice).

There is no possible way that Marc can create every annotation package that
people might like to have. At the end of the day, users such as yourself
will need to take the initiative and do what you need/would like to have for
yourself.

Cheers,
--Tony

On Tue, Oct 27, 2009 at 5:44 PM, Peng Yu <pengyu.ut at gmail.com> wrote:

> mogene10stprobeset.db is generated with AnnotationDbi for mouse gene
> array. I don't find a package that seems generated by AnnotationDbi
> for exon arrays on the webpage you mentioned. Is it correct?
>
> On Tue, Oct 27, 2009 at 7:00 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> > Hi Peng,
> >
> > I am not completely clear from your post what you want.  But most of our
> > annotation packages can be found here:
> >
> > http://www.bioconductor.org/packages/devel/data/annotation/
> >
> > If you don't find what you want, and you have gene accessions mapped
> > onto probes (something that should still be possible for an
> > exon-oriented platform), then you can use SQLForge in AnnotationDbi to
> > generate an annotation package.  To do so see the SQLForge vignette
> > which can be found in the AnnotationDbi package right here:
> >
> > http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.html
> >
> >
> >  Marc
> >
> >
> >
> >
> > Peng Yu wrote:
> >> There are gene level annotation for Gene Array mogene10stprobeset.db.
> >> I'm wondering if there are any package available for Exon Arrays?
> >>
> >> _______________________________________________
> >> 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
> >>
> >>
> >
> >
>
> ______________________________________________
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> PLEASE do read the posting guide
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>

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