[BioC] [R] Is there a package similar to mogene10stprobeset.db by for Affymetrix Exon Arrays?
pengyu.ut at gmail.com
Wed Oct 28 02:49:43 CET 2009
On Tue, Oct 27, 2009 at 8:33 PM, Tony Chiang <tchiang at fhcrc.org> wrote:
> 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.
Sorry, I typed the wrong mailing address.
> 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
I didn't ask Marc to create the package.
> 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?
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