Hi Tim and Steffen, You can also use the biomart attached to the http:// ncbi36.ensembl.org/ site using the following command: > mart = useMart("ENSEMBL_MART_ENSEMBL", host = "ncbi36.ensembl.org", dataset = "hsapiens_gene_ensembl") Checking attributes ... ok Checking filters ... ok This mart is release version 54. I hope that helps, Regards, Rhoda On 16 Oct 2009, at 18:18, Steffen at stat.berkeley.edu wrote: > Hi Tim, > > Do you specifically need Ensembl version 49 or would another Ensembl > version using NCBI36 do? > > The error is probably generated because 49 is old and some changes > to the > BioMart API occured after version 50 I think. You can access > Ensembl 54 > which is also using NCBI36, by doing the following: > > ensembl > = > useMart > (host="may2009.archive.ensembl.org",biomart="ENSEMBL_MART_ENSEMBL", > dataset="hsapiens_gene_ensembl") > > locations <- getBM(c('entrezgene','hgnc_symbol','chromosome_name', > + 'start_position','end_position'), > filters="entrezgene", > + values=entrezIDs, mart=ensembl) > >> locations > entrezgene hgnc_symbol chromosome_name start_position end_position > 1 10857 PGRMC1 X 118254279 118262456 > 2 5055 SERPINB2 18 59689906 59722100 > 3 8334 HIST1H2AC 6 26232352 26292434 > 4 8349 HIST2H2BE 1 148080395 148124826 > 5 85236 HIST1H2BK 6 27214052 27222598 > > > Note that you can find the correct host names to use for specific > Ensembl > versions by going to http://www.ensembl.org and then at the bottom > of the > page, click on "view in archive site", select an archive and then > copy the > url. > > Hope this helps, > Steffen > >> Hi, >> >> I wanted to query on the NCBI36 build, and built the following query: >> ---------------------------------------- >> entrezIDs <- c("8334","85236","10857","8349","5055") # sample list >> of ids >> ensembl <- useMart(biomart="ensembl", >> dataset="hsapiens_gene_ensembl",archive=TRUE) #"ensembl_mart_49" >> locations <- getBM(c('entrezgene','hgnc_symbol','chromosome_name', >> 'start_position','end_position'), >> filters="entrezgene", >> values=entrezIDs, mart=ensembl) >> _________________________________ >> >> >> I get the following error: >> Error in listFilters(mart, what = "type") : >> The function argument 'what' contains an invalid value: type >> Valid are: name, description, options, fullDescription, filters5, >> filters6 >> >> >> How should I modify the query? If I use the query with the current/ >> default >> version of ensembl, the query executes ok. >> thanks! >> My sessionInfo() is: >> ----------------- >> R version 2.9.1 (2009-06-26) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] grid stats graphics grDevices utils datasets >> methods >> [8] base >> >> other attached packages: >> [1] e1071_1.5-19 class_7.2-47 org.Hs.eg.db_2.2.11 >> [4] GOstats_2.10.0 graph_1.22.2 Category_2.10.1 >> [7] GO.db_2.2.11 biomaRt_2.0.0 multtest_2.1.1 >> [10] XML_2.5-3 genefilter_1.24.2 hgu133a.db_2.2.12 >> [13] RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.6.1 >> [16] GEOquery_2.8.0 RCurl_0.98-1 affy_1.22.0 >> [19] Biobase_2.4.1 gplots_2.7.1 caTools_1.9 >> [22] bitops_1.0-4.1 gdata_2.6.1 gtools_2.6.1 >> [25] lattice_0.17-25 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.12.0 annotate_1.22.0 GSEABase_1.6.1 >> [4] MASS_7.2-47 preprocessCore_1.6.0 RBGL_1.20.0 >> [7] splines_2.9.1 survival_2.35-4 tools_2.9.1 >> [10] xtable_1.5-5 >>> >> >> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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 Rhoda Kinsella Ph.D. Ensembl Bioinformatician, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.