Dear Rhoda, thank you so much: that solved the problem! best, Teresa ps: sorry, I already found your suggestion about changing the host to "www.ensembl.org" in a previous email, but [shame on me :D] was not able to find out how to do it! This time everything was crystal clear, I was able to fix my problem just repeating the exact same steps from you email. thanks! 2011/2/23 Rhoda Kinsella <rhoda at="" ebi.ac.uk="">: > Hi Teresa > Please try connecting to the Ensembl marts at Ensembl by using > host="www.ensembl.org". I have included my sessionInfo (I use an older > version), but please try my commands and see if you get the results you > need: > >> sessionInfo() > R version 2.9.2 (2009-08-24) > i386-apple-darwin8.11.1 > > locale: > en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> library(biomaRt) >> ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") >> dataset="hsapiens_gene_ensembl" >> ensembl=useDataset(dataset, mart=ensembl) > Checking attributes ... ok > Checking filters ... ok >> getBM("ensembl_gene_id", "hgnc_symbol", "FUS", ensembl) > ?ensembl_gene_id > 1 ENSG00000089280 >> > > I hope this helps > Regards > Rhoda > > > On 23 Feb 2011, at 12:13, Teresa Colombo wrote: > >> Hi, >> >> I am also having troubles with biomaRt since last Monday. I've been >> following threads on the topic in the Bioconductor mailing list these >> days trying to find a solution, but could not solve it yet. >> Following Jim suggestion's, today I tried updating R from version 2.11 >> to 2.12 and so the biomaRt package from 2.4 to 2.6, but this >> unfortunately did not solve the problem. >> >> Any further suggestion? >> >> thank you in advance, >> >> Teresa >> >> ____________________________ >> Teresa Colombo, PhD >> Dept of Cellular Biotechnology and Hematology >> 'Sapienza' University of Rome >> Phone/Fax: +39 06 4457731 >> >> >> >>> library(biomaRt) >>> mart <- useMart("ensembl","hsapiens_gene_ensembl") >>> getBM("ensembl_gene_id","hgnc_symbol", "FUS", mart) >> >> Errore in getBM("ensembl_gene_id", "hgnc_symbol", "FUS", mart) : >> ?Query ERROR: caught BioMart::Exception::Database: Could not connect >> to mysql database ensembl_mart_61: DBI >> >> connect('database=ensembl_mart_61;host=dcc-qa- db.oicr.on.ca;port=3306','bm_web',...) >> failed: Can't connect to MySQL server on 'dcc-qa-db.oicr.on.ca' (113) >> at >> /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm >> line 98 >>> >>> sessionInfo() >> >> R version 2.12.0 (2010-10-15) >> Platform: x86_64-redhat-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=it_IT.UTF-8 ? ? ? LC_NUMERIC=C >> [3] LC_TIME=it_IT.UTF-8 ? ? ? ?LC_COLLATE=it_IT.UTF-8 >> [5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=it_IT.UTF-8 >> [7] LC_PAPER=it_IT.UTF-8 ? ? ? LC_NAME=C >> [9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C >> [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] biomaRt_2.6.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.5-0 XML_3.2-0 >> >> >> >> >> >> >> >> 2011/2/22 James W. MacDonald <jmacdon at="" med.umich.edu="">: >>> >>> Hi Stephanie, >>> >>> >>> On 2/21/2011 6:29 PM, Stefanie Carola Gerstberger wrote: >>>> >>>> Hi all, >>>> I frequently use R biomaRt for querying ensembl. Over the weekend I >>>> experienced a problem with biomaRt. whatever I query I get >>>> >>>>> library(biomaRt) >>>>> ensembl=useMart("ensembl") >>>>> listDatasets(ensembl) >>>>> ens_sap=useMart("ensembl", dataset="hsapiens_gene_ensembl") >>>>> attr_sap=listAttributes(ens_sap) >>>>> filter_sap=listFilters(ens_sap) >>> >>> I get >>> >>>> library(biomaRt) >>>> mart <- useMart("ensembl","hsapiens_gene_ensembl") >>>> getBM("ensembl_gene_id","hgnc_symbol", "FUS", mart) >>> >>> ?ensembl_gene_id >>> 1 ENSG00000089280 >>>> >>>> sessionInfo() >>> >>> R version 2.12.0 Patched (2010-11-23 r53652) >>> Platform: x86_64-unknown-linux-gnu (64-bit) >>> >>> locale: >>> ?[1] LC_CTYPE=en_US.iso885915 ? ? ? LC_NUMERIC=C >>> ?[3] LC_TIME=en_US.iso885915 ? ? ? ?LC_COLLATE=en_US.iso885915 >>> ?[5] LC_MONETARY=C ? ? ? ? ? ? ? ? ?LC_MESSAGES=en_US.iso885915 >>> ?[7] LC_PAPER=en_US.iso885915 ? ? ? LC_NAME=C >>> ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? ? ? LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> other attached packages: >>> [1] biomaRt_2.6.0 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_1.5-0 XML_3.2-0 >>> >>> >>> What is the output of sessionInfo() for you? >>> >>> Best, >>> >>> Jim >>> >>> >>>>> >>>> >>>>> getBM(attributes="ensembl_gene_id", filters="hgnc_symbol", >>>>> values="FUS", >>>>> mart=ens_sap) >>>> >>>> Error in getBM(attributes = "ensembl_gene_id", filters = "hgnc_symbol", >>>> ?: >>>> ?Query ERROR: caught BioMart::Exception::Database: Could not connect to >>>> mysql >>>> database ensembl_mart_61: DBI >>>> >>>> >>>> connect('database=ensembl_mart_61;host=dcc-qa- db.oicr.on.ca;port=3306','bm_web',...) >>>> failed: Can't connect to MySQL server on 'dcc-qa-db.oicr.on.ca' (113) at >>>> >>>> >>>> /srv/biomart_server/biomart.org/biomart- perl/lib/BioMart/Configuration/DBLocation.pm >>>> line 98 >>>> >>>>> getBM(attributes="ensembl_gene_id", filters="refseq_dna", >>>>> values="NM_001134363", mart=ens_sap) >>>> >>>> >>>> I asked ensembl help desk and they advised me to use directly ensembl >>>> mart >>>> through this: >>>> >>>>> library(biomaRt) >>>>> ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") >>>>> dataset="hsapiens_gene_ensembl" >>>>> ensembl=useDataset(dataset, mart=ensembl) >>>> >>>> ..however when I try this command I get the following: >>>> >>>>> ensembl=useMart("ENSEMBL_MART_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 >>>> >>>> >>>> Does anyone know how to fix this problem? >>>> >>>> Thanks a lot, >>>> Stefanie >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> Douglas Lab >>> University of Michigan >>> Department of Human Genetics >>> 5912 Buhl >>> 1241 E. Catherine St. >>> Ann Arbor MI 48109-5618 >>> 734-615-7826 >>> ********************************************************** >>> Electronic Mail is not secure, may not be read every day, and should not >>> be >>> used for urgent or sensitive issues >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > Rhoda Kinsella Ph.D. > Ensembl Bioinformatician, > European Bioinformatics Institute (EMBL-EBI), > Wellcome Trust Genome Campus, > Hinxton > Cambridge CB10 1SD, > UK. > >