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

Aedin Culhane aedin at jimmy.harvard.edu
Thu Apr 21 05:15:33 CEST 2016

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 
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.

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.


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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