I'm using "AnnotationDbi" and "org.Mm.eg.db" in R to annotate gene ids of DE genes with both their gene symbol and entrez id. My original gtf file was downloaded from ensembl, so I'm using ensembl as the keytype.
For some of the genes it works, however for many instead of a symbol and ID it returns NA. I've googled a couple of the gene IDs that are returning NA and on their ensembl page they are all pseudogenes (not sure if this is a coincidence?).
Are pseudogenes not included in AnnotationDbi? Does anyone know how else to annotate gene ids to get their gene symbol and entrez id if so?