Hi,

I try to understand why the following does return "NA" :

library(annotate)
library(hgu133plus2.db)
get("1559804_at", hgu133plus2SYMBOL)

>NA

While a google search for probeset 1559804_at indicates ENSG00000253205 as a geneID

(see http://genecards.weizmann.ac.il/cgi-bin/geneannot/GA_search.pl?keyword_type=probe_set_list&keyword=1559804_at&array=HG-U133_Plus_2&target=integrated&.submit=Submit+Query for example)

I cannot understand why...

Thanks in advance for your help.

Nicolas

Please note that ENSG00000253205 is not HUGO symbol (which is what is mapped by the hgu133plus2SYMBOL BiMap) instead that is an Ensembl Gene ID.

The annotation packages for Bioconductor are mapped first to NCBI IDs  (usually GenBank/RefSeq or Entrez Gene IDs), and then mapped to all other annotations. Unfortunately, there are no NCBI IDs for this probe, other than a UniGene ID and the Ensembl Gene ID you show above (see here: https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=HG-U133_PLUS_2:1559804_AT).

If you want to use Ensembl based mappings, you can always use biomaRt:

> library(biomaRt)
> mart <- useMart("ensembl","hsapiens_gene_ensembl")
> getBM(c("affy_hg_u133_plus_2","ensembl_gene_id"), "affy_hg_u133_plus_2", "1559804_at", mart)
  affy_hg_u133_plus_2 ensembl_gene_id
1          1559804_at ENSG00000253205