[BioC] list of annaffy .db files?

[Marc Carlson]

Hi Andrew,

In addition to Vince's helpful comments, you can find a list of the
pre-made Bioconductor annotation packages here:

http://www.bioconductor.org/packages/devel/data/annotation/

And if you need to make your own .db package, you can use the SQLForge
vignette (which is also in the AnnotationDbi package).


  Marc



On 08/31/2010 07:57 AM, Vincent Carey wrote:
> there are no annaffy .db files -- the .db annotation paradigm is
> independent of annaffy
>
> see the annotationDbi vignette for more background
>
> for the ST array you can probably work from the package at
>
> http://www.bioconductor.org/packages/release/data/annotation/html/hugene10sttranscriptcluster.db.html
>
> but there is also a probeset version
>
> On Tue, Aug 31, 2010 at 10:46 AM, Andrew Einhorn
> <andreweinhorn at gmail.com> wrote:
>   
>> I am trying to use annaffy to annotate a hugene10stv1 array.  I cannot find
>> the name of the .db annotation packages I am supposed to install.  My code
>> thus far looks like:
>>
>> anncols <- aaf.handler()[c(1:4, 6,11)]
>> anntable <- aafTableAnn(rownames(exprs(results))[1:50], "insert package
>> name", anncols)
>>
>> Is there a list somewhere of the names of all the annaffy .db files?
>>
>> Regards
>>
>> Andrew
>>
>>        [[alternative HTML version deleted]]
>>
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