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Thanks Thomas,<br>
Indeed the problem was with the internet connection, I'll be careful
next time I connect from a coffee shop wiki spot ;)<br>
Best,<br>
Julien<br>
<br>
<div class="moz-cite-prefix">On 4/15/15 4:48 PM, Thomas Maurel
wrote:<br>
</div>
<blockquote
cite="mid:0D2D8E16-8448-4917-94A9-1107FCD5F383@ebi.ac.uk"
type="cite">
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Dear Julien,
<div class=""><br class="">
</div>
<div class="">Yes, this is the right place to post this since you
are querying the Ensembl marts on <a moz-do-not-send="true"
href="http://ensembl.org" class="">ensembl.org</a> ;-)</div>
<div class="">There is nothing wrong with your code, I’ve just
tried your query and got the result in few minutes:</div>
<blockquote style="margin: 0 0 0 40px; border: none; padding:
0px;" class="">
<div class="">
<div class="">> library("biomaRt")</div>
</div>
<div class="">
<div class="">> ensembl71 <- useMart(host='<a
moz-do-not-send="true"
href="http://apr2013.archive.ensembl.org" class="">apr2013.archive.ensembl.org</a>',
biomart='ENSEMBL_MART_ENSEMBL',
dataset='hsapiens_gene_ensembl')</div>
</div>
<div class="">
<div class="">> GO <- getBM(attributes=c(‘go_id',
'name_1006', 'namespace_1003'), mart = ensembl71)</div>
</div>
<div class="">> head(GO)</div>
<div class=""> go_id
name_1006 namespace_1003</div>
<div class="">1 GO:0007186 G-protein coupled receptor signaling
pathway biological_process</div>
<div class="">2 GO:0016021 integral to
membrane cellular_component</div>
<div class="">3 GO:0005886 plasma
membrane cellular_component</div>
<div class="">4 GO:0004930 G-protein coupled receptor
activity molecular_function</div>
<div class="">5 GO:0004984 olfactory receptor
activity molecular_function</div>
<div class="">6 GO:0008150
biological_process biological_process</div>
</blockquote>
<div class=""><br class="">
</div>
<div class="">It could be that our website our your internet
connection had a glitch. Could you please try again?</div>
<div class="">You could also try to update the BiomaRt package to
the current 2.20 version (<a moz-do-not-send="true"
href="http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html"
class="">http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html</a>)
and update your R software version.</div>
<div class="">It’s also good practice to refrain yourself from
running full genome queries with BioMart, an easy way around
this is to us filters to break down your query in smaller pieces
(e.g: to filter on chromosome names).</div>
<div class=""><br class="">
</div>
<div class="">Hope this helps,</div>
<div class="">Regards,</div>
<div class="">Thomas</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On 15 Apr 2015, at 15:34, Julien Roux <<a
moz-do-not-send="true" href="mailto:julien.roux@unil.ch"
class="">julien.roux@unil.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hi all,<br class="">
Not sure this is the right place to post this, please
redirect me if not.<br class="">
<br class="">
I'm having troubles retrieving data with biomaRt (2.18)
from Ensembl 71<br class="">
> library("biomaRt")<br class="">
> ensembl71 <- useMart(host='<a
moz-do-not-send="true"
href="http://apr2013.archive.ensembl.org" class="">apr2013.archive.ensembl.org</a>',
biomart='ENSEMBL_MART_ENSEMBL',
dataset='hsapiens_gene_ensembl')<br class="">
> GO <- getBM(attributes=c('go_id', 'name_1006',
'namespace_1003'), mart = ensembl71)<br class="">
Error in value[[3L]](cond) :<br class="">
Request to BioMart web service failed. Verify if you are
still connected to the internet. Alternatively the
BioMart web service is temporarily down.<br class="">
<br class="">
However the fwollowing commands work well, so I wonder if
the service is really down or if there is some other issue<br
class="">
> listFilters(ensembl71)<br class="">
> listAttributes(ensembl71)<br class="">
<br class="">
Best<br class="">
Julien<br class="">
<br class="">
-- <br class="">
Julien Roux<br class="">
Marie-Curie postdoctoral fellow<br class="">
Department of Ecology and Evolution, University of
Lausanne, Switzerland<br class="">
<a moz-do-not-send="true"
href="http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html"
class="">http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html</a><br
class="">
Tel: +41 78 700 2931<br class="">
<br class="">
<br class="">
_______________________________________________<br
class="">
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br class="">
Posting guidelines and subscribe/unsubscribe info:
<a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a><br class="">
</div>
</blockquote>
</div>
<br class="">
<div class="">
<div class="">
<div class="" style="orphans: 2; widows: 2;">--</div>
<div class="" style="orphans: 2; widows: 2;">Thomas Maurel<br
class="">
Bioinformatician - Ensembl Production Team<br class="">
European Bioinformatics Institute (EMBL-EBI)<br class="">
European Molecular Biology Laboratory<br class="">
Wellcome Trust Genome Campus<br class="">
Hinxton<br class="">
Cambridge CB10 1SD<br class="">
United Kingdom</div>
</div>
</div>
<br class="">
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Julien Roux
Marie-Curie postdoctoral fellow
Department of Ecology and Evolution, University of Lausanne, Switzerland
<a class="moz-txt-link-freetext" href="http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html">http://www.unil.ch/dee/home/menuinst/people/post-docs--associates/dr-julien-roux.html</a>
Tel: +41 78 700 2931
</pre>
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