[BioC] ecoli2.db

[Clémentine Dressaire]

Hello Marc,



After making sure that ecoli2.db was available in Bioconductor 2.7

released I tried several times today to install the package as follows and

got an error message

about ecoli2.db availability:



 source("http://bioconductor.org/biocLite.R")

BioC_mirror = http://www.bioconductor.org

Change using chooseBioCmirror().

>     biocLite("ecoli2.db") 

Using R version 2.12.0, biocinstall version 2.7.4.

Installing Bioconductor version 2.7 packages:

[1] "ecoli2.db"

Please wait...



Message d'avis :

In getDependencies(pkgs, dependencies, available, lib) :

  package ‘ecoli2.db’ is not available



Could you please tell me if I am doing something wrong of if this come

from a Bioconductor problem that you can fix?



Thanks for your precious help,



Clémentine









On Fri, 15 Oct 2010 09:09:40 -0700, Marc Carlson <mcarlson at fhcrc.org>

wrote:

> Hi Clémentine,

> 

> That is probably because I have dropped it into the devel branch.  I

> will become the release branch next week.  I think that most people are

> like you and will only care about the K12 strain.  But I have to post a

> disclaimer (and one is planned for when the package loads), simply

> because the probes on this platform were planned for detecting 4

> strains, and we only have annotation for the popular one here.

> 

> 

>   Marc

> 

> 

> 

> On 10/15/2010 02:10 AM, Clémentine Dressaire wrote:

>> 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