[Bioc-devel] new error(?) related to annotation: illuminaHumanv1CHR is deprecated

[Vincent Carey]

Thanks for the clarification.  Isn't there a way via active bindings to
preserve the
interfaces conferred by e.g., illuminaHumanv1CHRLOC, so that queries to the
object (no longer a Bimap) succeed with the endorsed metadata?  the chipDb
packages would be revised to use a new protocol for these queries that go
through
TxDb.

On Mon, Sep 22, 2014 at 8:38 PM, Marc Carlson <mcarlson at fhcrc.org> wrote:

> Hi Vince,
>
> So if you wanted to do this manually, then the thing you would want to do
> is to get a gene ID from the probe and to take that to a TranscriptDb
> object (again: that is if you wanted to do it manually).  Alternatively, if
> you had an OrganismDb object then this association would be handled for you
> (where it would be spelled out explicitly).  The explicit nature is what we
> are after here since where a gene is expected to be (chromosome wise) can
> depend on the build of genome you are using.  As people move between
> standard genomes and eventually to custom ones, we needed to decouple this
> kind of data from the organism packages (which are only ever intended to
> hold gene-centered data).
>
>  Marc
>
>
>
> On 09/21/2014 08:21 AM, Vincent Carey wrote:
>
>> On Sun, Sep 21, 2014 at 11:07 AM, Martin Morgan <mtmorgan at fhcrc.org>
>> wrote:
>>
>>  On 09/21/2014 07:44 AM, Vincent Carey wrote:
>>>
>>>  this is coming out of the build system for GGtools ... not easy to find
>>>> as
>>>> the
>>>>
>>>> problem seems to cause emission of megabytes of warnings
>>>>
>>>>
>>>> illuminaHumanv1CHR is deprecated as the data is better accessed from
>>>>
>>>>     another location. Please use an appropriate TxDb object or package
>>>> for
>>>>
>>>>     this kind of data.
>>>>
>>>>
>>>> i don't see the deprecation in the doc for illuminaHumanv1.db and i
>>>> cannot
>>>>
>>>> get a get() to throw it.  i also don't see this on the devel version
>>>> package landing page
>>>>
>>>>  Marc will likely reply on Monday. But the intention is that the CHR
>>> bimaps
>>> in *db packages Marc curates are being deprecated. The deprecation itself
>>> occurs in AnnotationDbi, I think. The reason is the lack of provenance
>>> for
>>> this information -- what genome build does it refer to? -- and its
>>> availability from other sources (i.e., the TxDb packages) with
>>> provenance.
>>>
>>>
>>>  Nice to hear about the streamlining and improved provenance.  I confess
>> I
>> don't
>> see how to get a probe-chr mapping out of TxDb -- is there something new
>> in
>> there?
>> A select operation that can resolve queries about manufacturer
>> identifiers?
>>
>>
>>  illuminaHumanv1CHR
>>>>
>>> illuminaHumanv1CHR is deprecated as the data is better accessed from
>>>    another location. Please use an appropriate TxDb object or package for
>>>    this kind of data.
>>> CHR map for chip illuminaHumanv1 (object of class "ProbeAnnDbBimap")
>>>
>>> I think this is currently a message, but should be a warning.
>>>
>>> AnnotationDbi is not building successfully, so its biocLite() version and
>>> landing page are not in sync with an svn checkout (used by the build
>>> system); to replicate on your own system requires an svn install, at
>>> least
>>> until AnnotationDbi builds successfully.
>>>
>>>  OK, so I can get the message now.  But I think more details need to be
>> supplied if
>> we are to drop references to *CHR.
>>
>>
>>  I guess the megabytes of warnings come from code in GGtools or elsewhere;
>>> maybe there's a
>>>
>>
>> Indeed.  Perhaps unrelated to this.
>>
>> convenient way of aggregating them (hopefully before throwing the warning,
>>
>>> since that can be quite expensive).
>>>
>>> Martin
>>>
>>>
>>>           [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>>  --
>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N.
>>> PO Box 19024 Seattle, WA 98109
>>>
>>> Location: Arnold Building M1 B861
>>> Phone: (206) 667-2793
>>>
>>>          [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
>

	[[alternative HTML version deleted]]