[BioC] ecoli2.db
Marc Carlson
mcarlson at fhcrc.org
Tue Oct 19 23:34:02 CEST 2010
Hi Clémentine,
The windows binary for ecoli2.db should be available now.
Marc
On 10/19/2010 11:03 AM, Clémentine Dressaire wrote:
> 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
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>
>
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