Great, that works. Thanks Steffen. I will send an email to the MGI support. best, Mike On Wed, Nov 6, 2013 at 2:48 PM, Steffen Durinck <durinck.steffen@gene.com>wrote: > Hi Mike, > > It looks like the MGI BioMart is not properly configured and someone > should make them aware of that. > > You can trick the biomaRt package to still get access to the BioMart > though, here's how: > > >mart=useMart("ensembl") > >mart@host="http://biomart.informatics.jax.org/biomart/martservice" > >mart@biomart="biomart" > > listDatasets(mart) > dataset description version > 1 markers Genes & Genome Features > 2 result Gene Expression Data (GXD) > > > mgi = useDataset("markers",mart=mart) > > listAttributes(mgi) > name description > 1 mgi_marker_id_att MGI ID > 2 marker_symbol_107 Feature Symbol > 3 marker_name_107 Feature Name > 4 marker_type_107 Feature Type > 5 synonym_1010 Feature Synonyms > 6 mouse_entrez_gene_id_108 Mouse Entrez Gene ID > > I haven't tried any query but I think this should work > > Best, > Steffen > > > > On Wed, Nov 6, 2013 at 9:48 AM, Michael Love <michaelisaiahlove@gmail.com>wrote: > >> hi, >> >> I'm trying to use the MGI BioMart at biomart.informatics.jax.org. I can >> listMarts: >> >> > listMarts(host="biomart.informatics.jax.org") >> biomart version >> 1 biomart MGI Biomart >> 2 ensembl Ensembl Mart 57 >> 3 vega VEGA 56 >> >> but cannot use any: >> >> > mart <- useMart("biomart",host="biomart.informatics.jax.org") >> Request to BioMart web service failed. Verify if you are still connected >> to >> the internet. Alternatively the BioMart web service is temporarily down. >> Check http://www.biomart.org and verify if this website is available. >> Error in if (BioMartVersion == "\n" | BioMartVersion == "") { : >> argument is of length zero >> Calls: useMart -> bmVersion >> >> The error is coming from this line in useMart, >> >> BioMartVersion = bmVersion(mart, verbose = verbose) >> >> ...which calls biomaRt:::bmVersion, and then the request is not a valid >> URL, >> >> request = paste(martHost(mart), "?type=version", >> "&requestid=biomaRt&mart=", >> martBM(mart), sep = "") >> >> ...because the martHost(mart) is given as "lindon": >> >> > listMarts("biomart","biomart.informatics.jax.org",includeHost=TRUE) >> $biomart >> [1] "biomart" "ensembl" "vega" >> >> $version >> [1] "MGI Biomart" "Ensembl Mart 57" "VEGA 56" >> >> $host >> [1] "lindon" "lindon" "lindon" >> >> $path >> [1] "/biomart/martservice" "/biomart/martservice" "/biomart/martservice" >> >> $database >> [1] "mgi_biomart" "ensembl_mart_57" "vega_mart_56" >> >> $port >> [1] "55555" "55555" "55555" >> >> $vschema >> [1] "default" "default" "default" >> >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-apple-darwin12.5.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_2.18.0 BiocInstaller_1.12.0 Defaults_1.1-1 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.95-4.1 tools_3.0.2 XML_3.98-1.1 >> >> >> thanks for any guidance, >> >> Mike >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]