Hi Thomas, That didn't work either. Although as I mentioned in my previous email, it does work if I use uswest.ensembl.org. The problem seems to be happening during a call to listMarts(host="www.ensembl.org", ... ). A request is sent to "http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt"; which returns
"<!DOCTYPE HTML PUBLIC \"-//IETF//DTD HTML 2.0//EN\">\n<html><head>\n<title>302 Found</title>\n</head><body>\n<h1>Found</h1>\n<p>The document has moved <a href=\"http://uswest.ensembl.org/biomart/martservice?type=registry&requestid=biomaRt;redirect=mirror;source=www.ensembl.org\";>here</a>.</p>\n</body></html>\n" The error occurs when an attempt to parse this using xmlTreeParse() is made. Cheers, Tyler On 2012-03-15, at 2:22 AM, Thomas Maurel wrote: > 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 >>>> >>> >>> >> >> _______________________________________________ >> Users mailing list >> [email protected] >> https://lists.biomart.org/mailman/listinfo/users > > -- > Thomas Maurel > Bioinformatician - Ensembl Production Team > European Bioinformatics Institute (EMBL-EBI) > Wellcome Trust Genome Campus, Hinxton > Cambridge - CB10 1SD - UK >
_______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
