I would like to construct a
RangedSummarizedExperiment from an
eSet) object (microarray data).
I can get an
eSet from GEO just fine:
perou2000_gse <- getGEO("GSE61", destdir = inputdatapath, GSEMatrix=TRUE) perou2000_eset@annotation # returns "GPL180"
and I can get basic annotation information for the array platform:
gse <- getGEO("GPL180").
(There is no bioc annotation pkg for this platform; I used the code listed in here Common workflow to build an microarray annatation package, like hgu133a.db) to test.)
What I would like to do is to construct a
RangedSummarizedExperiment object from the
eSet. My goal is to have functional annotation (Gene Symbol, GO term, etc..) but also positional annotation (James W. MacDonald | BiocAnno2016) so that I can do range-based queries.
My question is then how to proceed in order to construct an up-to-date and annotation-rich object around this microarray data?
My tentative approach is to take the genbank accession associated with each probe id (info returned by
getGEO("GPL180")) and get the respective sequences. Then, somehow, map them to the most recent version of the human genome and work out the rest of the annotation from the found genome locations? Is this how you would approach this problem?
Many thanks in advance