Hi Rhoda,
Yup I saw in a previous post that you had said that was a potential
workaround and tried that.
> ensembl <- useMart('ENSEMBL_MART_ENSEMBL',host="www.ensembl.org")
> ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
> gene.details<-getGene(id='ENSG00000163599',
type="ensembl_gene_id",mart=ensembl)
Error in martCheck(mart, "ensembl") :
This function only works when used with the ensembl BioMart.
So rather than rewrite a complicated function to use getBM I was going
to be patient... although it leads to the question as to why getGene()
function isn't supported on www.ensembl.org or is this just a feature of
biomaRt ?
Thanks for you help though.
O
On 29/05/13 08:59, Rhoda Kinsella wrote:
HI Oliver
Until this issue is resolved at www.biomart.org, you can point your host to
www.ensembl.org/biomart/martservice/ to get your data.
Hope that helps
Regards
Rhoda
On 29 May 2013, at 08:39, Oliver Burren <[email protected]> wrote:
Hi,
Not sure that this is the correct place to post but getting the following error
using biomaRt with following code. I notice that the host being returned is for
the BioMart portal hence why I'm posting here and not directly to Steffen.
Thanks for any help you can provide.
Olly Burren
#connect to BioMart
library(biomaRt)
ensembl <- useMart('ensembl')
ensembl <- useDataset("hsapiens_gene_ensembl",mart=ensembl)
gene.details<-getGene(id='ENSG00000163599', type="ensembl_gene_id",mart=ensembl)
Error in getBM(attributes = attrib, filters = type, values = id, mart = mart) :
Query ERROR: caught BioMart::Exception::Database: Could not connect to mysql
database ensembl_mart_71: DBI
connect('database=ensembl_mart_71;host=bm_mysql;port=3306','bmweb',...) failed:
Host '54.225.80.241' is blocked because of many connection errors; unblock with
'mysqladmin flush-hosts' at
/srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm
line 98
sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.16.0
loaded via a namespace (and not attached):
[1] RCurl_1.95-4.1 XML_3.96-1.1
_______________________________________________
Users mailing list
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Rhoda Kinsella Ph.D.
Ensembl Production Project Leader,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton,
Cambridge,
CB10 1SD
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