I have a list of ~31,000 mouse transcripts with their Ensembl transcript IDs that I'm trying to annotate using AnnotationDbi and the org.Mm.eg.db database. R v3.3.2, the object containing the IDs is called "temp". My command is:
mapIds(org.Mm.eg.db, keys=row.names(temp), keytype="ENSEMBLTRANS", column="SYMBOL", multiVals="first")
Only ~8500 get annotated with a gene name/symbol while the rest get "NA". If I search some of the NAs on Ensembl they match to transcripts/genes correctly. Some examples:
|Transcript ID from "temp"||Result from mapIDs||Link to Ensembl record|
You can see that even the 2 NAs have Ensembl transcript records so why are they not getting annotated by AnnotationDbi?
The command also outputs this, which I'm not sure is relevant or something to worry about:
'select()' returned 1:many mapping between keys and columns