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Question: biomaRt query
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gravatar for Tim Smith
8.0 years ago by
Tim Smith1.0k
Tim Smith1.0k wrote:
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]]
ADD COMMENTlink modified 8.0 years ago by steffen@stat.Berkeley.EDU600 • written 8.0 years ago by Tim Smith1.0k
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gravatar for steffen@stat.Berkeley.EDU
8.0 years ago by
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_MA RT_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 >
ADD COMMENTlink written 8.0 years ago by steffen@stat.Berkeley.EDU600
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.
ADD REPLYlink written 8.0 years ago by Rhoda Kinsella660
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