Hi Tyler
It looks like you are pointing to host www.biomart.org (this is the
default setting for accessing the marts using the biomaRt package) which
is still on Ensembl release 65. There was a new release on the main
Ensembl site (release 66) last week and this explains why you are seeing
differences when using the two resources. Please add host=www.ensembl.org
to allow you to access the most recent data.
Regards
Rhoda
> Hello I'm using the biomaRt package in R to map RefSeq mRNA ids to
> Ensemble Gene Ids.
> The code I'm using and an example of the results are as follows:
>
>> mart=useMart("ensembl", dataset="mmusculus_gene_ensembl")
>> getBM(attributes=c("refseq_mrna", "ensembl_gene_id"),
> + filters="refseq_mrna",
> + values="NM_175666",
> + mart=mart,
> + uniqueRows=T)
> refseq_mrna ensembl_gene_id
> 1 NM_175666 ENSMUSG00000058385
> 2 NM_175666 ENSMUSG00000047246
> 3 NM_175666 ENSMUSG00000018102
>>
>
> The result for the biomart web interface (and the ensembl site itself) is:
> NM_175666 ENSMUSG00000050936
>
> The Ensembl Gene Id above doesn't show up in the results from biomaRt.
>
> Are there any thoughts about what might be happening?
>
> Thank you,
> Tyler Funnell
>
>
>
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