Hi Tyler,
This should work:
mart <- useMart(biomart="ENSEMBL_MART_ENSEMBL",
dataset="mmusculus_gene_ensembl", host="www.ensembl.org",
path="/biomart/martservice")
Regards,
Thomas
On 15 Mar 2012, at 05:11, Tyler Funnell wrote:
> 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
>>>
>>
>>
>
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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK
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