[BioC] BrainArray custom CDF repository missing in biocReposList()
M Behnke
mkbehnke at gmail.com
Thu May 5 19:57:21 CEST 2011
Hello group,
Has anyone tried to use the updated brainarray files? I have searched
the mail lists and this is the most recent thread regarding them, and
I found no mention of changes in usage anywhere.
I updated to v14.1.0 for hgu133a2hsrefseq and it loads properly:
> library(hgu133a2hsrefseq.db)
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: org.Hs.eg.db
Loading required package: DBI
As it states in the instrurctions (and as it has worked before
updating), I enter the command
data at cdfName = 'hgu133a2hsrefseqREFSEQ'
But I get an error when attempting to do rma:
> data.rma=rma(data)
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain hgu133a2hsrefseqREFSEQ
Library - package hgu133a2hsrefseqrefseqcdf not installed
Bioconductor - hgu133a2hsrefseqrefseqcdf not available
This code has worked flawlessly before so I am not sure what is going
on as it appears to have installed and loaded properly!!
Thanks in advance for any help!
Here is my session info:
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] simpleaffy_2.28.0 gcrma_2.24.1
genefilter_1.34.0
[4] affy_1.30.0 hgu133a2hsrefseq.db_14.1.0
org.Hs.eg.db_2.5.0
[7] RSQLite_0.9-4 DBI_0.2-5
AnnotationDbi_1.14.1
[10] Biobase_2.12.1
loaded via a namespace (and not attached):
[1] affyio_1.20.0 annotate_1.30.0 Biostrings_2.20.0
IRanges_1.10.0
[5] preprocessCore_1.14.0 splines_2.13.0 survival_2.36-9
tools_2.13.0
[9] xtable_1.5-6
thanks,
Mikki
On Thu, Apr 21, 2011 at 2:59 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:
> Hi Diego,
>
> Your requests must have been persuasive since the maintainers at MBNI have
> just updated all of their packages again. And so there is now a version of
> these packages available for Bioconductor 2.8 (R 2.13).
>
> biocLite() has been updated accordingly and so now you should be able to get
> these packages in the very latest release of Bioconductor.
>
>
> Marc
>
>
> On 04/20/2011 08:54 PM, Diego Diez wrote:
>>
>> Hi Marc
>>
>> Of course, I understand (and support) the idea behind biocLite() and
>> that for the bioconductor installation to properly work it is needed
>> to ensure appropriate version of the packages to be installed. The
>> problem here is that the custom cdf packages are not - to the best of
>> my understanding- official bioconductor packages, but the repository
>> is provided in biocReposList() as a convenience. Therefore the lack of
>> support for custom cdf packages in this bioconductor version was not
>> mentioned in the release announcement. It may have been worth
>> mentioning since this may have a big impact on users.
>>
>> Obviously, removing the repository while not suitable packages exists
>> makes all the sense. However, biocReposList() also provides a
>> repository for cran, and any package present in cran will be installed
>> by biocLite() whether it is compatible with the bioconductor version
>> or not. Even there is a recent thread in the list about an old (non
>> compatible) version of the graph package present in cran being
>> installed because the official one was missing in the repositories.
>> Unfortunately I cannot think on a way to overcome this limitation.
>> That being said I myself never had a problem using biocLite() on a
>> number of year of use.
>>
>> Two additional comments:
>>
>> - The help page for biocReposList() might be a bit old since it lists
>> two repositories not presently found:
>> -----------
>> oh : URL for Bioc Omegahat package repository. This repository
>> contains the versions of Omegahat packages that were tested
>> with the current Bioc release.
>>
>> li : URL for Bioc Lindsey package repository.
>> ------------
>>
>> whereas the repository "extra" is missing.
>>
>> - The cran repository is forced to be "http://cran.fhcrc.org".
>> Wouldn't be better to try to get the default CRAN repository selected
>> by the user in case that option is set?
>>
>>
>> Anyway, to finish this lengthy email just let you know that I
>> contacted the custom cdf people and they are working on providing
>> packages for bioconductor 2.8 soon!
>>
>> Diego
>>
>>
>> On Thu, Apr 21, 2011 at 1:55 AM, Marc Carlson<mcarlson at fhcrc.org> wrote:
>>>
>>> Hi Diego,
>>>
>>> You can always throw caution to the wind and just forcibly install any
>>> tarball (if downloaded manually). Although that would be taking matters
>>> into your own hands, and you would obviously have to live with any of the
>>> consequences that might result.
>>>
>>> But you should *not* normally be able to get these package using
>>> biocLite()
>>> if there is not an appropriate version available. This is because
>>> correct
>>> version matching is part of what people depend on when using biocLite().
>>> And in this case the problem is indeed because of the issue that you
>>> mentioned. The .db packages would have been built using sources
>>> appropriate
>>> for the Bioc 2.7 and so if you installed them with Bioc 2.8, the GO and
>>> KEGG
>>> terms etc. would be out of sync with the rest of the build.
>>>
>>> It is also true that the cdf and probe packages might be ok for some
>>> things
>>> in Bioc 2.8. But without the corresponding .db package you will not
>>> really
>>> be able to really use them fully. And if you did use them and then tried
>>> to
>>> use those remapped probe and cdf packages with the wrong (default) .db
>>> style
>>> packages the result could be quite chaotic. So I can't really recommend
>>> that either unless you have some very specialized usage in mind.
>>>
>>>
>>> Marc
>>>
>>>
>>>
>>>
>>> On 04/19/2011 07:29 PM, Diego Diez wrote:
>>>>
>>>> Hi Marc
>>>>
>>>> On Wed, Apr 20, 2011 at 1:10 AM, Marc Carlson<mcarlson at fhcrc.org>
>>>> wrote:
>>>>>
>>>>> Hi Diego,
>>>>>
>>>>> The brainarray CDFs are only missing from the 2.8 build of Bioconductor
>>>>> because there is not yet a brainarray build that matches that. There
>>>>> is
>>>>> a
>>>>> recent brainarray build that matches Bioconductor 2.7 though, so we
>>>>> have
>>>>> of
>>>>> course provided access to that for the older 2.7 branch.
>>>>
>>>> Do you mean that the recent brainarray build was not generated using
>>>> the latest versions of the framework in Bioconductor 2.8 (like GO.db,
>>>> KEGG.db, etc.)? Because other than that I can install those packages
>>>> without problem in R2.13/Bioc2.8. I imagine this may create some
>>>> problems with unmatched entries...
>>>>
>>>>> If you are interested in access to a set of brainarray packages that
>>>>> match
>>>>> Bioconductor 2.8, then I would recommend that you contact them and let
>>>>> them
>>>>> know how much you appreciate their hard work. ;)
>>>>
>>>> I will, since I really appreciate their hard work!
>>>>
>>>>> We will of course make such packages available as soon as it is
>>>>> possible
>>>>> to
>>>>> do so.
>>>>
>>>> Thank you for the clarification.
>>>>
>>>> Diego
>>>>
>>>>> Marc
>>>>>
>>>>>
>>>>> On 04/18/2011 11:20 PM, Diego Diez wrote:
>>>>>>
>>>>>> Hi all,
>>>>>>
>>>>>> I noticed that the mirror for the custom CDFs available at the
>>>>>> BrainArray Microarray laboratory is missing in BioC 2.8, and wonder
>>>>>> whether this is intentional and permanent.
>>>>>>
>>>>>> Thank you,
>>>>>>
>>>>>> --
>>>>>> Diego Diez, PhD
>>>>>> Bioinformatics center,
>>>>>> Institute for Chemical Research,
>>>>>> Kyoto University.
>>>>>> Gokasho, Uji, Kyoto 611-0011 JAPAN
>>>>>> diez at kuicr.kyoto-u.ac.jp
>>>>>>
>>>>>>
>>>>>>> library(Biobase)
>>>>>>
>>>>>> Welcome to Bioconductor
>>>>>>
>>>>>> Vignettes contain introductory material. To view, type
>>>>>> 'browseVignettes()'. To cite Bioconductor, see
>>>>>> 'citation("Biobase")' and for packages 'citation("pkgname")'.
>>>>>>
>>>>>>> biocReposList()
>>>>>>
>>>>>> bioc
>>>>>> "http://bioconductor.org/packages/2.8/bioc"
>>>>>> aData
>>>>>> "http://bioconductor.org/packages/2.8/data/annotation"
>>>>>> eData
>>>>>> "http://bioconductor.org/packages/2.8/data/experiment"
>>>>>> extra
>>>>>> "http://bioconductor.org/packages/2.8/extra"
>>>>>> cran
>>>>>> "http://cran.fhcrc.org"
>>>>>>>
>>>>>>> sessionInfo()
>>>>>>
>>>>>> R version 2.13.0 Patched (2011-04-13 r55441)
>>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>>>>
>>>>>> locale:
>>>>>> [1] C/UTF-8/C/C/C/C
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>>
>>>>>> other attached packages:
>>>>>> [1] Biobase_2.12.1
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor at r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>
>>>
>
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