error with accessing biomaRt attributes
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@kishor-tappita-2563
Last seen 8.1 years ago
Dear List, I get the below error while trying to access biomaRt attributes. > getBM(attributes = c("entrezgene"),values = c("202763_at","209310_s_at"),mart =ensembl) Error in getBM(attributes = c("entrezgene"), values = c("202763_at", "209310_s_at"), : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list. > sessionInfo() R version 2.9.2 (2009-08-24) 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] stats graphics grDevices utils datasets methods base other attached packages: [1] RCurl_0.98-1 bitops_1.0-4.1 gene2pathway_1.2.0 org.Dm.eg.db_2.2.11 RBGL_1.20.0 graph_1.22.2 KEGGSOAP_1.18.0 [8] biomaRt_2.0.0 KEGG.db_2.2.11 RSQLite_0.7-2 DBI_0.2-4 AnnotationDbi_1.6.1 Biobase_2.4.1 kernlab_0.9-8 loaded via a namespace (and not attached): [1] SSOAP_0.4-6 tools_2.9.2 XML_2.5-1 Thanks, Kishor
biomaRt biomaRt • 1.2k views
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@steve-lianoglou-2771
Last seen 23 days ago
United States
Hi, On Sep 16, 2009, at 3:47 AM, Kishor Tappita wrote: > Dear List, > > I get the below error while trying to access biomaRt attributes. > > >> getBM(attributes = c("entrezgene"),values = c >> ("202763_at","209310_s_at"),mart =ensembl) > Error in getBM(attributes = c("entrezgene"), values = c("202763_at", > "209310_s_at"), : > The query to the BioMart webservice returned an invalid result: > biomaRt expected a character string of length 1. Please report this to > the mailing list. Aren't you forgetting to pass in the "filters" parameter to the getBM function? It looks like you're trying to get an entrezgene id from some affy probe id? You have to tell the function what types of "things" you're passing into "values" using the "filter" param. Look closely (again) at the code in the Example section of ?getBM -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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Dear Steve, Thank you for your reply. You are right I am trying to convery Affy Id to entrez gene ID. Passing the filters parameter to the query solved my problem. Below is the modified query. getBM(attributes = "entrezgene",values = c("1007_s_at","1053_at","1552256_a_at"),filters= "affy_hg_u133_plus_2",mart =ensembl) Thanks, Kishor On Wed, Sep 16, 2009 at 8:15 PM, Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> wrote: > Hi, > > On Sep 16, 2009, at 3:47 AM, Kishor Tappita wrote: > >> Dear List, >> >> I get the below error while trying to access biomaRt attributes. >> >> >>> getBM(attributes = c("entrezgene"),values = >>> c("202763_at","209310_s_at"),mart =ensembl) >> >> Error in getBM(attributes = c("entrezgene"), values = c("202763_at", >> "209310_s_at"), ?: >> The query to the BioMart webservice returned an invalid result: >> biomaRt expected a character string of length 1. Please report this to >> the mailing list. > > Aren't you forgetting to pass in the "filters" parameter to the getBM > function? > > It looks like you're trying to get an entrezgene id from some affy probe id? > You have to tell the function what types of "things" you're passing into > "values" using the "filter" param. > > Look closely (again) at the code in the Example section of ?getBM > > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > ?| ?Memorial Sloan-Kettering Cancer Center > ?| ?Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > >
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Chao-Jen Wong ▴ 580
@chao-jen-wong-3603
Last seen 7.8 years ago
USA/Seattle/Fred Hutchinson Cancer Reseā€¦
Hi, Kishor, How did you generate the object 'ensembl'? Can you double check to see whether it is a valid, non-empty biomaRt object? Kishor Tappita wrote: > Dear List, > > I get the below error while trying to access biomaRt attributes. > > > >> getBM(attributes = c("entrezgene"),values = c("202763_at","209310_s_at"),mart =ensembl) >> > Error in getBM(attributes = c("entrezgene"), values = c("202763_at", > "209310_s_at"), : > The query to the BioMart webservice returned an invalid result: > biomaRt expected a character string of length 1. Please report this to > the mailing list. > > > >> sessionInfo() >> > R version 2.9.2 (2009-08-24) > 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] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] RCurl_0.98-1 bitops_1.0-4.1 gene2pathway_1.2.0 > org.Dm.eg.db_2.2.11 RBGL_1.20.0 graph_1.22.2 > KEGGSOAP_1.18.0 > [8] biomaRt_2.0.0 KEGG.db_2.2.11 RSQLite_0.7-2 > DBI_0.2-4 AnnotationDbi_1.6.1 Biobase_2.4.1 > kernlab_0.9-8 > > loaded via a namespace (and not attached): > [1] SSOAP_0.4-6 tools_2.9.2 XML_2.5-1 > > Thanks, > Kishor > > _______________________________________________ > 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 > -- Chao-Jen Wong Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Avenue N., M2-B876 PO Box 19024 Seattle, WA 98109 206.667.4485 cwon2 at fhcrc.org
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