[BioC] BrainArray custom CDF repository missing in biocReposList()
James W. MacDonald
jmacdon at med.umich.edu
Thu May 5 21:06:55 CEST 2011
Hi Mikki,
First off, please don't hijack other threads. This doesn't have anything
to do with the CDF repository for the MBNI cdfs. When you have a new
question, send a new email to the list.
On 5/5/2011 1:57 PM, M Behnke wrote:
> 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'
I would be interested to know what instructions advise you to do this.
In addition, I would be shocked if this ever actually worked for you
(because it really never should have).
What you want to be doing is
abatch <- ReadAffy(cdfname = "hgu133a2hsrefseq")
data.rma <- rma(abatch)
and proceeding from there.
You might also reconsider using 'data' as a variable name, as data() is
a function from base R, so you are relying on R to divine what you mean
when you type data at an R prompt. It's usually pretty good, but why
take chances?
Best,
Jim
>
> 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
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>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>
>>>>
>>
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>
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--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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