[BioC] BrainArray custom CDF repository missing in biocReposList()

[Marc Carlson]

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
>>>
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