[BioC] ecoli2.db

[Marc Carlson]

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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>