after performing a differential expression analysis on a set of .CEL files downloaded from GEO, I'm trying to map the Affymetrix Probe IDs to GeneSymbols using the 'annotate' package with 'hgu133plus2.db'. However, from ~150 significant genes, about 50 can't be mapped ("NA"), which I think is quite a lot. Even more concerning, the top 5 genes can't be mapped.
I also tried using Probe IDs instead of the GeneSymbols when performing GO-enrichment analysis with DAVID, but they don't seem to mapped at all, when choosing AFFYMETRIX_3PRIME_IVT_ID.
My questions are:
Why is that? Shouldn't all IDs map?
How am I supposed proceed from here on? I doesn't feel right to simply exclude all "NA" Genes from further analysis's.
Any help is greatly appreciated.