Hi, I'm analysing Affymetrix Clariom D microarray data and have a question about annotation.
While annotating data with pd.clariom.d.human, I had a problem with genes that mapped to the same probe. If I annotate with this package, R takes only the first of the multiple genes. Even if I use annotateEset() with multivals= "list", R returns the first value.
I tried to use clariomdhumantranscriptcluster.db, but this package caused an issue of a different kind: some probes were mapped to more genes than they should be. I realised this when comparing my results with Transcriptome Analysis Console's annotation (TAC). For example, TC0X00007229.hg.1 in TAC was mapped to GAGE12F, GAGE12J, GAGE12D, GAGE5, GAGE6, GAGE12B, GAGE4, GAGE2E. Whereas when I used select() from AnnotationDbi, the probe was mapped to GAGE12F, GAGE12J, GAGE12D, GAGE5, GAGE6, GAGE12B, GAGE4, GAGE12G, GAGE12I, GAGE7 (GAGE2E was not identified).
And I cannot use select() from AnnotationDbi, because my data has an AffyHTAPDInfo signature, not ChipDb. I would like to know how to properly annotate my data and identify all genes with proper mappings.
