[Bioc-devel] Bioc-devel Digest, Vol 145, Issue 60

Vincent Carey stvjc at channing.harvard.edu
Fri Apr 22 14:31:07 CEST 2016

On Thu, Apr 21, 2016 at 8:35 AM, Martin Morgan <
martin.morgan at roswellpark.org> wrote:

> On 04/20/2016 11:15 PM, Aedin Culhane wrote:
>> Hi Vince
>> Agreed, I agree fData is over-simplification. But if data have an
>> associated "annotation", the feature annotation associated with it
>> should be available.
>> I was recently trying to map between one of the hugene st1.0 and
>> primeview arrays.  The first has multiple .db packages  (including
>> hugene10stprobeset.db,
>> hugene10sttranscriptcluster.db) and its not very clear which is the
>> correct one to use.   There is no .db package for primeview, so I had to
>> download the .csv file from the Affy website and build the package.
> so auto-filling annotations wouldn't have helped here, because there is
> not an automatic choice between alternate packages and because the
> primeview array doesn't have an annotation package?
> The probe genome co-ordinates would allow better merging of platforms
>> (as opposed to mapping identifiers to a common entrez gene id/transcript
>> id). Moreover, with GRanges, we could use mapToTranscripts,
>> findOverlaps, countOverlaps to map between platforms.
> the brain array project makes it clear that there's more than one way to
> map a probe to a gene. All we do is report what the manufacturer says. I
> think we don't have the resources (technical expertise, in addition to
> labor) to re-inventing and maintain our own mappings.

Yes.  I think there are two threads emerging here.

First, one focused on support for affy arrays.  We've lost momentum here
but may still be the system of first resort for people
who want to preprocess and analyze them.  More vignettes and benchmarking
for the newer releases like HTA and primeview
would probably be welcome to researchers who use them (120 GDS in GEO for
primeview, one of which cites affy/RMA;  82 GDS on HTA 2.0 gene version).
I think someone who is heavily invested in these platforms would have to
step up to fill gaps in our support.

Second, the concept of streamlining the attachment of annotation
information to array or sequence-based quantifications.
Here we need data from the community about current gaps and successes.  I
think it would be helpful (and feasible) to have
a generic that addresses this, but there is variation in the number of
resources to be consulted to annotate a given platform, and no natural
choice of resource for various types of feature.   So programming and
documentation at the user level seem inevitable for any given solution.
Centralized efforts may not pay off.

> Martin
>> A.
>> On 4/20/16 22:20, Vincent Carey wrote:
>>> I am in favor of simplifying the binding of useful metadata to our
>>> genome-wide objects.  Before we automate this I think we
>>> should define a widely applicable procedure for this task ... and see
>>> how it works in examples from the ExperimentData library and
>>> ExperimentHub.  Using fData for ExpressionSet and rowData for
>>> SummarizedExperiment and rowRanges for RangedSummarizedExperiment
>>> might also be susceptible of simplification.  fAnno?
>>> On Wed, Apr 20, 2016 at 4:10 PM, Aedin Culhane
>>> <aedin at jimmy.harvard.edu <mailto:aedin at jimmy.harvard.edu>> wrote:
>>>      Hi
>>>      Using select/mapIDs to annotate probe IDs is an additional step
>>>      that confuses many.
>>>      May I suggest we automatically populate fData with minimal
>>>      annotation (ProbeID, entrez ID, symbol) if a known platform is
>>>      detected.   We record the version and parameters (eg mapIDs
>>>      multi=first) used to create fData.  But for beginners I think it
>>>      would be a helpful start.
>>>      What do you think?
>>>      Aedin
>>>      _______________________________________________
>>>      Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org> mailing
>>>      list
>>>      https://stat.ethz.ch/mailman/listinfo/bioc-devel
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