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