[BioC] biomaRt query

Sean Davis sdavis2 at mail.nih.gov
Wed Dec 10 03:49:59 CET 2008

On Tue, Dec 9, 2008 at 7:21 PM, Sebastien Gerega <seb at gerega.net> wrote:
> Hi,
> there is probably a very simple answer to this question but why does the
> following code produce the output NULL?
> ensembl = useMart("ensembl", dataset="hsapiens_gene_ensembl")
> getBM(attributes = c("entrezgene", "hgnc_symbol"), filters = "entrezgene",
> values = "117581", mart = ensembl, na.value = NA)
> The NCBI site has a hgnc symbol listed for the gene:
> http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=117581

If you do a similar search at Ensembl, it appears that Ensembl does
not have an entry for TWIST2.  (I did the search quickly, so I could
be mistaken.)  Remember that these genome databases do not always
agree about what a gene represents (or even which ones exist).


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