Hello,
When I tried this, I got an error:
> mart = useMart("ensembl", dataset="mmusculus_gene_ensembl",
> host="www.ensembl.org")
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
>
I did some digging and this is caused by the server returning an HTML redirect
notice instead of the expected XML during a call to listMarts. Using
useMart("ENSEMBL_MART_ENSEMBL="mmusculus_gene_ensembl",
host="uswest.ensembl.org") did the trick.
On 2012-03-07, at 12:12 AM, [email protected] wrote:
> 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
>>
>>
>>
>> _______________________________________________
>> Users mailing list
>> [email protected]
>> https://lists.biomart.org/mailman/listinfo/users
>>
>
>
_______________________________________________
Users mailing list
[email protected]
https://lists.biomart.org/mailman/listinfo/users
