[BioC] affylmGUI/biocReposList() Problem

[Dan Tenenbaum]

P.S. The brainarray thing is just a warning, and you can ignore it
unless you really need some of those brain array packages.
Dan


On Thu, Jul 5, 2012 at 4:01 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> It looks like affylmGUI (maintainer CC'd) still has a lot of calls to
> Biobase:::biocReposList() which is indeed a defunct function. It
> should use BiocInstaller biocinstallRepos() instead.
>
> Dan
>
>
> On Thu, Jul 5, 2012 at 2:47 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
>> Hi Burkhard,
>>
>> Well, that all looks OK. So the next likely culprit is affylmGUI itself.
>> Since you are not getting the gene symbols, it would be reasonable to assume
>> that affylmGUI is trying to download and install the correct annotation
>> package.
>>
>> You don't say what chip data you are analyzing, so I can't give much more
>> than a generalized pointer. If it is an old-school 3'-biased chip (like the
>> HG-U133 plus 2 chip), then you can usually get really close to the right
>> name by just reducing to lower case and removing all punctuation, then
>> adding a .db, so e.g, hgu133plus2.db is the annotation package. If you are
>> using a Gene ST package, then you want to do the same, but add
>> transcriptcluster.db. So e.g., the HuGene 1.0 ST chip annotation package is
>> the hugene10sttranscriptcluster.db.
>>
>> So try installing the correct annotation package first, then do your
>> analysis. See if that helps.
>>
>> Best,
>>
>> Jim
>>
>>
>>
>> On 7/5/2012 4:54 PM, Burkhard Heil wrote:
>>>
>>> Hi Jim,
>>>
>>> Thanks for your quick reply. Here is the Output of sessionInfo:
>>>
>>>
>>> sessionInfo()
>>> R version 2.15.1 (2012-06-22)
>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] tcltk     stats     graphics  grDevices utils     datasets  methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] affylmGUI_1.30.0   affyio_1.24.0      affy_1.34.0
>>> Biobase_2.16.0
>>> [5] BiocGenerics_0.2.0 limma_3.12.1       stringr_0.6
>>>
>>> loaded via a namespace (and not attached):
>>> [1] BiocInstaller_1.4.7   plyr_1.7.1            preprocessCore_1.18.0
>>> [4] zlibbioc_1.2.0
>>> Cheers
>>> Burkhard
>>>
>>>
>>> On 05.07.2012, at 21:05, "James W. MacDonald"<jmacdon at uw.edu>  wrote:
>>>
>>>
>>>> HI Burkhard,
>>>>
>>>> On 7/5/2012 9:24 AM, Burkhard Heil wrote:
>>>>>
>>>>> Hi everybody,
>>>>>
>>>>> when trying to calculate the Toptable in affylmGUI there pops the
>>>>> following error message up:
>>>>>
>>>>> Error: The biocReposList() function is defunct. Please use biocLite() to
>>>>> install packages source("http://bioconductor.org/biocLite.R")
>>>>> biocLite("<pkgname>") if you really need to get the list of Bioconductor
>>>>> package repositories (like biocReposList() does), then do:
>>>>> source("http://bioconductor.org/biocLite.R") biocinstallRepos()
>>>>>
>>>>> The Toptable ist still calculated but without the Gene Symbols. When I
>>>>> call biocLite() from R, it tries to install the packages 'Biobase' 'IRanges'
>>>>> and 'AnnotationDbi'. Sounds to me that the last one is causing the problem.
>>>>> Also, biocLite complains that it can't access
>>>>> "http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.15".
>>>>> I read the post about that problem and changed the mirror via
>>>>> chooseBioCmirror(). biocLite still looks for the brainarray adress but then
>>>>> install from another mirror. But everytime I call biocLite it installs those
>>>>> 3 packges.
>>>>>
>>>>> I'm running R 2.15.1 on OS X Lion. AffylmGUI and all the relevant
>>>>> packages should have the most recent version.
>>>>
>>>> Should have? That's not very reassuring. Why don't you load affylmGUI,
>>>> run sessionInfo() and then post the output.
>>>>
>>>> Best,
>>>>
>>>> Jim
>>>>
>>>>
>>>>> Any help would be greatly appreciated! Thanks
>>>>>
>>>>> Burkhard
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor at r-project.org
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>>>>> Search the archives:
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>>>>
>>>> --
>>>> James W. MacDonald, M.S.
>>>> Biostatistician
>>>> University of Washington
>>>> Environmental and Occupational Health Sciences
>>>> 4225 Roosevelt Way NE, # 100
>>>> Seattle WA 98105-6099
>>>>
>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> University of Washington
>> Environmental and Occupational Health Sciences
>> 4225 Roosevelt Way NE, # 100
>> Seattle WA 98105-6099
>>
>> _______________________________________________
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