[BioC] Having trouble with new brainarray CDF
M Behnke
mkbehnke at gmail.com
Thu May 5 21:33:01 CEST 2011
My apologies, the subject line and discussion were about the
brainarray CDFs and the fact that they were now updated, and my
problem is with the updates so the background seemed appropriate.
I've changed the subject line now.
Thank you for responding so quickly, however, using the code you
suggest gives me the same error:
> abatch <- ReadAffy(cdfname = "hgu133a2hsrefseq")
> data.rma <- rma(abatch)
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain hgu133a2hsrefseq
Library - package hgu133a2hsrefseqcdf not installed
Bioconductor - hgu133a2hsrefseqcdf not available
I got my original code from the paper referenced on the brainarray website
http://nar.oxfordjournals.org/content/33/20/e175.full?ijkey=zaJMV7qU1XANIci&keytype=ref
under the section "Use of custom CDF"
The previous version (2.12 and appropriate cdf) continues to work with
either code.
I checked help(package=...) to make sure I wasn't referencing it wong,
but I don't see any problems with the names...
Information on package 'hgu133a2hsrefseq.db'
Description:
Package: hgu133a2hsrefseq.db
Title: Affymetrix hgu133a2 annotation data (chip
hgu133a2hsrefseq)
Description: Affymetrix hgu133a2 annotation data (chip
hgu133a2hsrefseq) assembled using data from public
repositories
Version: 14.1.0
Author: Marc Carlson, Seth Falcon, Herve Pages, Nianhua Li
Maintainer: Biocore Data Team <biocannotation at lists.fhcrc.org>
Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.14.1),
org.Hs.eg.db (>= 2.5.0)
Suggests: annotate
Imports: methods, AnnotationDbi
License: Artistic-2.0
organism: Homo sapiens
species: Human
manufacturer: Affymetrix
chipName: hgu133a2
manufacturerUrl: http://www.affymetrix.com
biocViews: AnnotationData, AffymetrixChip, Homo_sapiens,
hgu133a2hsrefseq
Packaged: 2011-04-21 03:01:18 UTC; daimh
Built: R 2.13.0; ; 2011-05-05 17:36:07 UTC; windows
Index:
hgu133a2hsrefseq.db Bioconductor annotation data package
hgu133a2hsrefseqREFSEQ
Map between Manufacturer Identifiers and RefSeq
Identifiers
hgu133a2hsrefseqSYMBOL
Map between Manufacturer Identifiers and Gene
Symbols
Thanks again!
Mikki
On Thu, May 5, 2011 at 3:06 PM, James W. MacDonald
<jmacdon at med.umich.edu> wrote:
> 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
>>>>>>>
>>>>>
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
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>>
>> _______________________________________________
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>
> --
> James W. MacDonald, M.S.
> Biostatistician
> Douglas Lab
> University of Michigan
> Department of Human Genetics
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