Thank you Martin, Tim and Steve!!

For future readers, the introduction section of this document
here<http://www.bioconductor.org/packages/2.12/bioc/vignettes/AnnotationForge/inst/doc/MakingNewAnnotationPackages.pdf>
(written
by Marc Carlson) throws some light on the purpose of having select
interfaces/annotation packages.

-Sashi


On Sat, May 11, 2013 at 7:33 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote:

> On 05/10/2013 01:17 AM, Rameswara Sashi Kiran Challa wrote:
>
>> Hi All,
>>
>> Could anyone please elucidate advantages of having an Annotation package
>> for an organism or point me to any documentation that clearly lists all
>> the
>> various thoughts behind coming up with an Annotation package.
>>
>> Will not having a data frame in R (with rows as genes and columns as
>> various types of annotations like GO, KEGG, Unigene, etc) suffice? What
>> are
>>
>
> One aspect not mentioned is that one gets to exploit R's packaging system
> to provide easily distributed and documented versions of the data. Suppose
> you created the package eight months ago and have forgotten some of the
> detaiils. Easy, check out the package description and help page. Say you're
> working with a couple of colleagues, and you've been relatively disciplined
> about incrementing the annotation package when your data changes (or are
> using a public Bioc annotation package, with versions strictly tied to R /
> Bioc releases). Easily spot when unusual results are due to differences in
> data version (hence the frequent request for the output of 'sessionInfo()'
> on this mailing list) and adopt / instill 'best practices' that make sure
> everyone on the team (including yourself, even if your team is only 1) are
> using the same version.
>
> Martin
>
>  the advantages of having a AnnodbBimap objects and building a package? Are
>> there any technical benefits like faster access of information?
>>
>> Thanks for your time,
>>
>> -Sashi
>>
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