[BioC] ecoli2.db

[Marc Carlson]

Hi Clémentine,

There is both an org package for E coli and also a .db0 package.  The
existence of the .db0 package means that you can use the vignette titled
"SQLForge: An easy way to create a new annotation package with a
standard database schema." in the AnnotationDbi package to generate a
chip package for E coli.  You can find it here:

http://www.bioconductor.org/help/bioc-views/devel/bioc/html/AnnotationDbi.html

But since this is an affymetrix package, I just went ahead and added an
ecoli2 chip package to the repository for you. 

Be forewarned though, that while this platform has probes to measure 4
different strains of E coli, I can only used the annotations for the
popular K12 strain to make this package.  If you want to get additional
annotations for the other strains, you might be able to get one more in
a separate package (if one of the strains is the Sakai strain), but
after that things become much more difficult to support...  Be sure to
let us know whether or not this meets your needs.  The annotations are
always a work in progress and we always benefit from feedback to
indicate what people are using, and what things might be missing.


  Marc




On 10/14/2010 02:43 AM, Clémentine Dressaire wrote:
> Dear BioC members,
>
>
>
> I was looking for a ecoli2.db annotation file but could not find it in
>
> Bioconductor (or elsewhere). From previous posts I saw that some people
>
> have already asked for this and were considering creating one. Can anyone
>
> tell me if such a work is in process or still a project? If not I will try
>
> to create my own. Is SQLForge package the most appropriated for this
>
> purpose taking into account that I only have Affymetrix annotation file?
>
>
>
> With adavanced thanks for your help,
>
>
>
> Clémentine.
>
>
>
>