Thanks Steffen Aedin Steffen at stat.Berkeley.EDU wrote: > It looks like the central repository at www.biomart.org doesn't work at the > moment. This is what biomaRt uses as default server. > > You could reroute and use www.ensembl.org as webservice until the central > service is fixed. Below an example to reroute: > > > >> listMarts(host="www.ensembl.org") >> > biomart version > 1 ENSEMBL_MART_ENSEMBL Ensembl 55 > 2 ENSEMBL_MART_SNP Ensembl variation 55 > 3 ENSEMBL_MART_FUNCGEN Ensembl functional genomics 55 > 4 ENSEMBL_MART_VEGA Vega 35 > 5 REACTOME Reactome (CSHL US) > 6 wormbase_current WormBase (CSHL US) > 7 pride PRIDE (EBI UK) > >> mart = >> > useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl",host= "www.ensembl.org") > Checking attributes ... ok > Checking filters ... ok > > > Once you're connected you via www.ensembl.org you should be able to do > your queries. > > Cheers, > Steffen > > >> I am getting a biomaRt error. it works last night, but is failing today. >> >> > library(biomaRt) >> > example(getBM) >> >> getBM> if(interactive()){ >> getBM+ mart <- useMart("ensembl") >> getBM+ datasets <- listDatasets(mart) >> getBM+ mart<-useDataset("hsapiens_gene_ensembl",mart) >> getBM+ >> getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name" ,"band"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_a t"), >> mart=mart) >> getBM+ >> getBM+ } >> Checking attributes and filters ... ok >> >> V1 >> 1 Query ERROR: caught BioMart::Exception::Database: Error during query >> execution: Can't find file: >> './ensembl_mart_55/hsapiens_gene_ensembl__ox_AFFY_HG_U95Av2__dm.frm' >> (errno: 13) >> Error in getBM(attributes = c("affy_hg_u95av2", "hgnc_symbol", >> "chromosome_name", : >> Number of columns in the query result doesn't equal number of >> attributes in query. This is probably an internal error, please report. >> >> > sessionInfo() >> R version 2.9.0 (2009-04-17) >> i486-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_1.16.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_0.94-1 XML_1.93-2 >> >> -- >> Aed?n Culhane, >> Research Associate >> Computational Biology and Functional Genomics Laboratory >> Harvard School of Public Health, Dana-Farber Cancer Institute >> >> 44 Binney Street, SM822C >> Department of Biostatistics and Computational Biology, >> Dana-Farber Cancer Institute >> Boston, MA 02115 >> USA >> >> Phone: +1 (617) 632 2468 >> Fax: +1 (617) 582 7760 >> Email: aedin at jimmy.harvard.edu >> Web URL: http://www.hsph.harvard.edu/research/aedin-culhane/ >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > > -- Aed?n Culhane, Research Associate Computational Biology and Functional Genomics Laboratory Harvard School of Public Health, Dana-Farber Cancer Institute 44 Binney Street, SM822C Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute Boston, MA 02115 USA Phone: +1 (617) 632 2468 Fax: +1 (617) 582 7760 Email: aedin at jimmy.harvard.edu Web URL: http://www.hsph.harvard.edu/research/aedin-culhane/