[BioC] retrieve gene symbol/description

[Sean Davis]

On Wed, Apr 18, 2012 at 3:08 PM, array chip <arrayprofile at yahoo.com> wrote:
> Hi, I am trying to retrieve gene symbol/description with GenBank/EMBL IDs using biomaRt. I was successful with some IDs, but not with others. For example:
>
>> library(biomaRt)
>
>> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
>
>
>> getBM(attributes=c('embl', 'description','hgnc_symbol'),   filters = 'embl', values = c('AF133587','AA456140'), mart = ensembl)
>
>       embl                                                          description hgnc_symbol
> 1 AF133587 rhabdoid tumor deletion region gene 1 [Source:HGNC Symbol;Acc:13437]       RTDR1
>
>
> As you can see, the first ID returns gene symbol/description successfully, but the 2nd one did not. What is the reason for the 2nd one not working? Is there other ways to get it to work?
>

Hi, John.

This query is working as expected.  The genbank accession "AA456140"
is not associated with any gene in the Ensembl gene collection.  Try
typing your two accessions into the ensembl search box.  You'll note
that one the first is associated with a gene while the second is
simply a genomic alignment (and not associated with a gene).

Sean