[BioC] ecoli2.db

Marc Carlson mcarlson at fhcrc.org
Tue Oct 19 19:50:40 CEST 2010


Hi Clémentine,

I am still building the Mac binaries for this, so the issue might be
caused by the fact that (so far) only the tarball is available.  It
would help me if you gave the output of sessionInfo() so that I know
what version of things you are even using.  If you are using Mac or
Windows and don't want to wait till later in the day when I get those
binaries built, you can  try this (which should work):

biocLite("ecoli2.db", type="source")

And if that doesn't help you, then please use sessionInfo() and get back
to me.


  Marc



On 10/19/2010 07:21 AM, Clémentine Dressaire wrote:
> 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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>>>>     
>>>>         
>>>       
>



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