[BioC] ecoli2.db
Clémentine Dressaire
clementinedressaire at itqb.unl.pt
Tue Oct 19 20:03:29 CEST 2010
Hello again,
Here is the outpout of my sessionInfo():
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C
[5] LC_TIME=French_France.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ecoli2cdf_2.6.0 simpleaffy_2.26.0 gcrma_2.22.0
[4] genefilter_1.32.0 annotate_1.28.0 biomaRt_2.6.0
[7] GOstats_2.16.0 graph_1.28.0 Category_2.16.0
[10] annaffy_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5
[13] RSQLite_0.9-2 DBI_0.2-5 AnnotationDbi_1.12.0
[16] lattice_0.19-13 affy_1.28.0 Biobase_2.10.0
[19] limma_3.6.0
loaded via a namespace (and not attached):
[1] affyio_1.18.0 Biostrings_2.18.0 grid_2.12.0
[4] GSEABase_1.12.0 IRanges_1.8.0 preprocessCore_1.12.0
[7] RBGL_1.25.1 RCurl_1.4-4.1 splines_2.12.0
[10] survival_2.35-8 tools_2.12.0 XML_3.2-0.1
[13] xtable_1.5-6
I hope it will help you. I do not have time to try the trick today but
thanks anyway,
Clémentine
On Tue, 19 Oct 2010 10:50:40 -0700, Marc Carlson <mcarlson at fhcrc.org>
wrote:
> 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.
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at stat.math.ethz.ch
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>>
>>>>
>>
--
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
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