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
<ae...@jimmy.harvard.edu <mailto:ae...@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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