Dear All,

I run the following code with my dataset res in order to transfer REFSEQ identifiers into ENTREZIDs. It was successful. However, about 30,000 of REFSEQ IDs like XP_047XXXXXX (for example, XP_047283139, XP_047284854, XP_047293471...) did not return ENTREZIDs. I randomly checked some of these REFSEQ at NCBI databases, and found that they do have ENTREZIDs.

Could you please tell me whether org.Hs.eg.db has REFSEQ IDs like XP_047XXXXXX? If yes, whether these REFSEQ IDs have the corresponding ENTREZIDs within org.Hs.eg.db? How to transfer these REFSEQ IDs into ENTREZIDs?

res$entrez = mapIds(org.Hs.eg.db,
                    keys=row.names(res), 
                    column="ENTREZID",
                    keytype="REFSEQ",
                    multiVals="first")

The RefSeq IDs you show in your question are protein isoform IDs. org.Hs.eg.db contains gene IDs. It does not contain protein isoform IDs.