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