Hi Tim,

By default getBM queries go to the central BioMart service, they are
lagging a bit behind with the Ensembl version that they host and are
running v69.  If you do your query on the latest version of Ensembl you get
results for one more of your ids:

mart <- useMart("ENSEMBL_MART_ENSEMBL",
dataset="hsapiens_gene_ensembl",host="www.ensembl.org")
attr <- c("refseq_mrna",'hgnc_symbol',
'chromosome_name','start_position','end_position')
ids <- c("NM_001270493", "NM_001185076","NM_001185075","NM_001185082")
xx <- getBM(attributes=attr,filters = "refseq_mrna", values = ids, mart =
mart)
> xx
   refseq_mrna hgnc_symbol chromosome_name start_position end_position
1 NM_001185075        FMR1               X      146993469    147032645
2 NM_001185076        FMR1               X      146993469    147032645
3 NM_001185082        FMR1               X      146993469    147032645

The missing id NM_001270493 might be to novel to have been included in the
latest Ensembl build.  To find out for sure you could email the Ensembl
helpdesk at helpdesk@ensembl,org

Cheers,
Steffen



On Fri, May 24, 2013 at 4:46 AM, Tim Smith <tim_smith_666@yahoo.com> wrote:

> Hi,
>
> I was trying to get the gene details of refseq ids (these are output from
> blastn) with the following code:
>
> =================
>
>   library(biomaRt)
>   mart <- useMart("ensembl", dataset="hsapiens_gene_ensembl")
>   attr <- c("refseq_mrna",'hgnc_symbol',
> 'chromosome_name','start_position','end_position')
>   ids <- c("NM_001270493", "NM_001185076","NM_001185075","NM_001185082")
>
>   xx <- getBM(attributes=attr,
>               filters = "refseq_mrna", values = ids, mart = mart)
>
>   print(xx)
> ===============
>
> The results are:
> >   print(xx)
>    refseq_mrna hgnc_symbol chromosome_name start_position end_position
> 1 NM_001185075        FMR1               X      146993469    147032645
> 2 NM_001185076        FMR1               X      146993469    147032645
>
>
> How can I get details of the other two refseq ids that do not show up in
> the results?
>
>
> thanks!
>
> Tim
>
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>
>
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