[BioC] ecoli2.db

[Clémentine Dressaire]

Dear Marc,



Since I work with the MG1655 (K12) strain it should be enough for me to

have only annotations for this one. 

Nevertheless I cannot find the ecoli2 chip package you added neither in

Bioconductor website nor using AnnotationDbi package in R. Does it mean

that it has not been released yeat or that I have to use the ecoliK12.db0?

Unlesss I am not looking in the right place?



Thanks for your help, be sure it is usefull!



Clémentine





On Thu, 14 Oct 2010 13:50:43 -0700, Marc Carlson <mcarlson at fhcrc.org>

wrote:

> 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.

>>

>>

>>

>>

> 

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-- 

Clémentine Dressaire

Post-doctoral research fellow

Control of gene expression lab

ITQB - Instituto de Tecnologia Química e Biológica

Apartado 127, Av. da República

2780-157 Oeiras

Portugal

+351 214469562