From the looks of it, it seems that biomaRt is not handling the
redirection properly. I guess if you visit www.ensembl.org from US/Ca,
it redirects you to the local installation (uswest.ensembl.org) and
redirection response is what you see below.
Best,
Syed
On 15/03/2012 17:21, Tyler Funnell wrote:
Hi Thomas,
That didn't work either. Although as I mentioned in my previous email,
it does work if I use uswest.ensembl.org <http://uswest.ensembl.org>.
The problem seems to be happening during a call to
listMarts(host="www.ensembl.org <http://www.ensembl.org>", ... ).
A request is sent to
"http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
<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\
<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
<http://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 <http://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 <http://uswest.ensembl.org/>") did the trick.
On 2012-03-07, at 12:12 AM, [email protected] <mailto:[email protected]>
wrote:
Hi Tyler
It looks like you are pointing to host www.biomart.org
<http://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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--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK
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