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

[Martin Morgan]

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.

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
>>
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>>
>
>
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