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

[Marc Carlson]

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
>>
>>
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