Hi Mikki,

Have you tried also updating the matching cdf file (as suggested by the 
error message: "Library - package hgu133a2hsrefseqcdf not installed")? 
IOW:|||

source("http://bioconductor.org/biocLite.R")|
biocLite("hgu133a2hsrefseqcdf")


   Marc



On 05/05/2011 12:33 PM, M Behnke wrote:
> 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@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@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@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@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@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@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@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@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@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@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@r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>> --
>> 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
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and should not be
>> used for urgent or sensitive issues
>>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


	[[alternative HTML version deleted]]

