biomart error
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Natasha ▴ 440
@natasha-4640
Last seen 9.6 years ago
Dear List, I am using biomaRt for the first time. Initially I had problems connecting to hsapiens dataset, though I could listMarts. However that issue was resolved (by solutions in some earlier posts) by changing the host to www.ensembl.org. Now though I get the following error message when I try to execute the following command: >mg_eg.ens.t <- getBM(attributes = c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbol" ), filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) V1 1 <head> 2 <link rel="Shortcut" icon="" href="/errors/ensembl_ico.png" type="image/png"/> 3 The Ensembl Genome Browser 4 <style type="text/css"> 5 body{color:#333333;background-color:#eaeeff;font- family:Arial,Helvetica,Sans-serif;font-size:14pt;margin:0;padding:0} 6 #masthead{color:#ffffff;background- color:#333366;width:100%;height:50px;padding:5px 0;font-size:1.75em;text-align:center;margin:auto} Error in getBM(attributes = c("entrezgene", "ensembl_gene_id", "ensembl_transcript_id", : The query to the BioMart webservice returned an invalid result: the number of columns in the result table does not equal the number of attributes in the query. Please report this to the mailing list. This I found strange as I did the same thing yesterday with another object and it worked!! Full Code and SessionInfo: headmg.u.eg$Entrez_Gene_ID) #[1] 27122 3488 72 1293 100134134 390 lengthmg.u.eg$Entrez_Gene_ID) #[1] 4288 listMarts(host="www.ensembl.org") ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") listDatasets(ensembl) ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", dataset="hsapiens_gene_ensembl") filt = listFilters(ensembl) atts = listAttributes(ensembl) mg_eg.ens <- getBM(attributes = c("entrezgene","ensembl_gene_id","hgnc_symbol"), filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) # 4016 3 mg_eg.ens.t <- getBM(attributes = c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbol" ), filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.8.0 DESeq_1.4.1 locfit_1.5-6 lattice_0.19-23 [5] akima_0.5-4 Biobase_2.12.1 WriteXLS_2.1.0 gdata_2.8.2 [9] limma_3.8.2 loaded via a namespace (and not attached): [1] annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5 [4] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0 [7] gtools_2.6.2 RColorBrewer_1.0-2 RCurl_1.6-4 [10] RSQLite_0.9-4 splines_2.13.0 survival_2.36-5 [13] tools_2.13.0 XML_3.4-0 xtable_1.5-6 Many Thanks, Natasha --
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@herve-pages-1542
Last seen 10 hours ago
Seattle, WA, United States
Hi Natasha, Not sure that is actually the cause of your problem but you might want to update your installation to use the latest versions of packages (e.g. your RCurl and biomaRt are not the latest). Instructions on how to update are here: http://bioconductor.org/install/ The problem might be something else but it doesn't hurt to keep your installation up-to-date, all the contrary. Cheers, H. On 11-08-18 03:02 AM, Natasha Sahgal wrote: > Dear List, > > I am using biomaRt for the first time. > > Initially I had problems connecting to hsapiens dataset, though I could > listMarts. However that issue was resolved (by solutions in some earlier > posts) by changing the host to www.ensembl.org. > > Now though I get the following error message when I try to execute the > following command: > > >mg_eg.ens.t <- getBM(attributes = > c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbo l"), > filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) > > > V1 > 1 <head> > 2 <link rel="Shortcut" icon="" href="/errors/ensembl_ico.png" type="image/png"/> > 3 The Ensembl Genome Browser > 4 <style type="text/css"> > 5 > body{color:#333333;background-color:#eaeeff;font- family:Arial,Helvetica,Sans-serif;font-size:14pt;margin:0;padding:0} > > 6 > #masthead{color:#ffffff;background- color:#333366;width:100%;height:50px;padding:5px > 0;font-size:1.75em;text-align:center;margin:auto} > Error in getBM(attributes = c("entrezgene", "ensembl_gene_id", > "ensembl_transcript_id", : > The query to the BioMart webservice returned an invalid result: the > number of columns in the result table does not equal the number of > attributes in the query. Please report this to the mailing list. > > > This I found strange as I did the same thing yesterday with another > object and it worked!! > > Full Code and SessionInfo: > > headmg.u.eg$Entrez_Gene_ID) #[1] 27122 3488 72 1293 100134134 390 > > lengthmg.u.eg$Entrez_Gene_ID) #[1] 4288 > > > listMarts(host="www.ensembl.org") > ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") > listDatasets(ensembl) > ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", > dataset="hsapiens_gene_ensembl") > filt = listFilters(ensembl) > atts = listAttributes(ensembl) > > mg_eg.ens <- getBM(attributes = > c("entrezgene","ensembl_gene_id","hgnc_symbol"), filters = "entrezgene", > values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) # 4016 3 > > mg_eg.ens.t <- getBM(attributes = > c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbo l"), > filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) > > sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.8.0 DESeq_1.4.1 locfit_1.5-6 lattice_0.19-23 > [5] akima_0.5-4 Biobase_2.12.1 WriteXLS_2.1.0 gdata_2.8.2 > [9] limma_3.8.2 > > loaded via a namespace (and not attached): > [1] annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5 > [4] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0 > [7] gtools_2.6.2 RColorBrewer_1.0-2 RCurl_1.6-4 > [10] RSQLite_0.9-4 splines_2.13.0 survival_2.36-5 > [13] tools_2.13.0 XML_3.4-0 xtable_1.5-6 > > > Many Thanks, > Natasha > > -- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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Natasha ▴ 440
@natasha-4640
Last seen 9.6 years ago
Dear All, Please ignore this, as now it does appear to work. I do wonder, why did it not work earlier though. Also, could someone please tell me the difference between "with_illumina_humanht_12" and "illumina_humanht_12" in the filters and attributes? What version of the illumina_humanht_12 chip is used, as this is unclear? Many Thanks, Natasha On 18/08/2011 11:02, Natasha Sahgal wrote: > Dear List, > > I am using biomaRt for the first time. > > Initially I had problems connecting to hsapiens dataset, though I > could listMarts. However that issue was resolved (by solutions in some > earlier posts) by changing the host to www.ensembl.org. > > Now though I get the following error message when I try to execute the > following command: > > >mg_eg.ens.t <- getBM(attributes = > c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbo l"), > filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) > > > > V1 > 1 <head> > 2 <link rel="Shortcut" icon="" href="/errors/ensembl_ico.png" type="image/png"/> > 3 The Ensembl Genome Browser > 4 <style type="text/css"> > 5 > body{color:#333333;background-color:#eaeeff;font- family:Arial,Helvetica,Sans-serif;font-size:14pt;margin:0;padding:0} > 6 > #masthead{color:#ffffff;background- color:#333366;width:100%;height:50px;padding:5px > 0;font-size:1.75em;text-align:center;margin:auto} > Error in getBM(attributes = c("entrezgene", "ensembl_gene_id", > "ensembl_transcript_id", : > The query to the BioMart webservice returned an invalid result: the > number of columns in the result table does not equal the number of > attributes in the query. Please report this to the mailing list. > > > This I found strange as I did the same thing yesterday with another > object and it worked!! > > Full Code and SessionInfo: > > headmg.u.eg$Entrez_Gene_ID) #[1] 27122 3488 72 > 1293 100134134 390 > > lengthmg.u.eg$Entrez_Gene_ID) #[1] 4288 > > > listMarts(host="www.ensembl.org") > ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") > listDatasets(ensembl) > ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", > dataset="hsapiens_gene_ensembl") > filt = listFilters(ensembl) > atts = listAttributes(ensembl) > > mg_eg.ens <- getBM(attributes = > c("entrezgene","ensembl_gene_id","hgnc_symbol"), filters = > "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) # > 4016 3 > > mg_eg.ens.t <- getBM(attributes = > c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbo l"), > filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) > > sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 > [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.8.0 DESeq_1.4.1 locfit_1.5-6 lattice_0.19-23 > [5] akima_0.5-4 Biobase_2.12.1 WriteXLS_2.1.0 gdata_2.8.2 > [9] limma_3.8.2 > > loaded via a namespace (and not attached): > [1] annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5 > [4] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0 > [7] gtools_2.6.2 RColorBrewer_1.0-2 RCurl_1.6-4 > [10] RSQLite_0.9-4 splines_2.13.0 survival_2.36-5 > [13] tools_2.13.0 XML_3.4-0 xtable_1.5-6 > > > Many Thanks, > Natasha > > -- > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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Natasha, On 11-08-18 06:32 AM, Natasha Sahgal wrote: > Dear All, > > Please ignore this, as now it does appear to work. I do wonder, why did > it not work earlier though. > > Also, could someone please tell me the difference between > "with_illumina_humanht_12" and "illumina_humanht_12" in the filters and > attributes? I don't see the "with_illumina_humanht_12" attribute: library(biomaRt) ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", dataset="hsapiens_gene_ensembl") atts = listAttributes(ensembl) Then: > atts[grep("illumina", atts[[1]], ignore.case=TRUE), ] name description 104 illumina_humanwg_6_v1 Illumina HumanWG 6 v1 105 illumina_humanwg_6_v2 Illumina HumanWG 6 v2 106 illumina_humanwg_6_v3 Illumina HumanWG 6 v3 107 illumina_humanht_12 Illumina Human HT 12 > What version of the illumina_humanht_12 chip is used, as this is unclear? According to the Illumina website the latest version of this chip seems to be v4 but it's not clear indeed that the Emsembl folks are referring to that one. You might want to ask them directly (biomaRt is just a tool to query data their data). Cheers, H. > > > Many Thanks, > Natasha > > On 18/08/2011 11:02, Natasha Sahgal wrote: >> Dear List, >> >> I am using biomaRt for the first time. >> >> Initially I had problems connecting to hsapiens dataset, though I >> could listMarts. However that issue was resolved (by solutions in some >> earlier posts) by changing the host to www.ensembl.org. >> >> Now though I get the following error message when I try to execute the >> following command: >> >> >mg_eg.ens.t <- getBM(attributes = >> c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symb ol"), >> filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) >> >> >> V1 >> 1 <head> >> 2 <link rel="Shortcut" icon="" href="/errors/ensembl_ico.png" type="image/png"/> >> 3 The Ensembl Genome Browser >> 4 <style type="text/css"> >> 5 >> body{color:#333333;background-color:#eaeeff;font- family:Arial,Helvetica,Sans-serif;font-size:14pt;margin:0;padding:0} >> >> 6 >> #masthead{color:#ffffff;background- color:#333366;width:100%;height:50px;padding:5px >> 0;font-size:1.75em;text-align:center;margin:auto} >> Error in getBM(attributes = c("entrezgene", "ensembl_gene_id", >> "ensembl_transcript_id", : >> The query to the BioMart webservice returned an invalid result: the >> number of columns in the result table does not equal the number of >> attributes in the query. Please report this to the mailing list. >> >> >> This I found strange as I did the same thing yesterday with another >> object and it worked!! >> >> Full Code and SessionInfo: >> >> headmg.u.eg$Entrez_Gene_ID) #[1] 27122 3488 72 1293 100134134 390 >> >> lengthmg.u.eg$Entrez_Gene_ID) #[1] 4288 >> >> >> listMarts(host="www.ensembl.org") >> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") >> listDatasets(ensembl) >> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", >> dataset="hsapiens_gene_ensembl") >> filt = listFilters(ensembl) >> atts = listAttributes(ensembl) >> >> mg_eg.ens <- getBM(attributes = >> c("entrezgene","ensembl_gene_id","hgnc_symbol"), filters = >> "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) # 4016 3 >> >> mg_eg.ens.t <- getBM(attributes = >> c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symb ol"), >> filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) >> >> sessionInfo() >> R version 2.13.0 (2011-04-13) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] biomaRt_2.8.0 DESeq_1.4.1 locfit_1.5-6 lattice_0.19-23 >> [5] akima_0.5-4 Biobase_2.12.1 WriteXLS_2.1.0 gdata_2.8.2 >> [9] limma_3.8.2 >> >> loaded via a namespace (and not attached): >> [1] annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5 >> [4] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0 >> [7] gtools_2.6.2 RColorBrewer_1.0-2 RCurl_1.6-4 >> [10] RSQLite_0.9-4 splines_2.13.0 survival_2.36-5 >> [13] tools_2.13.0 XML_3.4-0 xtable_1.5-6 >> >> >> Many Thanks, >> Natasha >> >> -- >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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Dear Herve, Thanks for this. Though with "with_illumina_humanht_12" and "illumina_humanht_12" are definitely in the filters. listMarts(host="www.ensembl.org") ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", dataset="hsapiens_gene_ensembl") filt = listFilters(ensembl) filt[grep("illumina", filt[[1]], ignore.case=TRUE), ] name description 12 with_illumina_humanwg_6_v1 with Illumina HumanWG 6 v1 ID(s)) 13 with_illumina_humanwg_6_v2 with Illumina HumanWG 6 v2 ID(s) 14 with_illumina_humanwg_6_v3 with Illumina HumanWG 6 v3 ID(s) 15 with_illumina_humanht_12 with Illumina Human HT 12 ID(s) 125 illumina_humanwg_6_v1 Illumina HumanWG 6 V1 ID(s) [e.g. 0000940471] 126 illumina_humanwg_6_v2 Illumina HumanWG 6 V2 ID(s) [e.g. ILMN_1748182] 127 illumina_humanwg_6_v3 Illumina HumanWG 6 v3 ID(s) [e.g. ILMN_2103362] 128 illumina_humanht_12 Illumina Human HT 12 ID(s) [e.g. ILMN_1672925] Many Thanks, Natasha On 18/08/2011 15:04, Hervé Pagès wrote: > Natasha, > > On 11-08-18 06:32 AM, Natasha Sahgal wrote: >> Dear All, >> >> Please ignore this, as now it does appear to work. I do wonder, why did >> it not work earlier though. >> >> Also, could someone please tell me the difference between >> "with_illumina_humanht_12" and "illumina_humanht_12" in the filters and >> attributes? > > I don't see the "with_illumina_humanht_12" attribute: > > library(biomaRt) > ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", > dataset="hsapiens_gene_ensembl") > atts = listAttributes(ensembl) > > Then: > > > atts[grep("illumina", atts[[1]], ignore.case=TRUE), ] > name description > 104 illumina_humanwg_6_v1 Illumina HumanWG 6 v1 > 105 illumina_humanwg_6_v2 Illumina HumanWG 6 v2 > 106 illumina_humanwg_6_v3 Illumina HumanWG 6 v3 > 107 illumina_humanht_12 Illumina Human HT 12 > >> What version of the illumina_humanht_12 chip is used, as this is >> unclear? > > According to the Illumina website the latest version of this chip seems > to be v4 but it's not clear indeed that the Emsembl folks are referring > to that one. You might want to ask them directly (biomaRt is just a tool > to query data their data). > > Cheers, > H. > >> >> >> Many Thanks, >> Natasha >> >> On 18/08/2011 11:02, Natasha Sahgal wrote: >>> Dear List, >>> >>> I am using biomaRt for the first time. >>> >>> Initially I had problems connecting to hsapiens dataset, though I >>> could listMarts. However that issue was resolved (by solutions in some >>> earlier posts) by changing the host to www.ensembl.org. >>> >>> Now though I get the following error message when I try to execute the >>> following command: >>> >>> >mg_eg.ens.t <- getBM(attributes = >>> c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_sym bol"), >>> >>> filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = >>> ensembl) >>> >>> >>> V1 >>> 1 <head> >>> 2 <link rel="Shortcut" icon="" href="/errors/ensembl_ico.png">>> type=image/png /> >>> 3 The Ensembl Genome Browser >>> 4 <style type="text/css"> >>> 5 >>> body{color:#333333;background-color:#eaeeff;font- family:Arial,Helvetica,Sans-serif;font-size:14pt;margin:0;padding:0} >>> >>> >>> 6 >>> #masthead{color:#ffffff;background- color:#333366;width:100%;height:50px;padding:5px >>> >>> 0;font-size:1.75em;text-align:center;margin:auto} >>> Error in getBM(attributes = c("entrezgene", "ensembl_gene_id", >>> "ensembl_transcript_id", : >>> The query to the BioMart webservice returned an invalid result: the >>> number of columns in the result table does not equal the number of >>> attributes in the query. Please report this to the mailing list. >>> >>> >>> This I found strange as I did the same thing yesterday with another >>> object and it worked!! >>> >>> Full Code and SessionInfo: >>> >>> headmg.u.eg$Entrez_Gene_ID) #[1] 27122 3488 72 1293 100134134 390 >>> >>> lengthmg.u.eg$Entrez_Gene_ID) #[1] 4288 >>> >>> >>> listMarts(host="www.ensembl.org") >>> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") >>> listDatasets(ensembl) >>> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", >>> dataset="hsapiens_gene_ensembl") >>> filt = listFilters(ensembl) >>> atts = listAttributes(ensembl) >>> >>> mg_eg.ens <- getBM(attributes = >>> c("entrezgene","ensembl_gene_id","hgnc_symbol"), filters = >>> "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) # 4016 3 >>> >>> mg_eg.ens.t <- getBM(attributes = >>> c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_sym bol"), >>> >>> filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = >>> ensembl) >>> >>> sessionInfo() >>> R version 2.13.0 (2011-04-13) >>> Platform: x86_64-pc-linux-gnu (64-bit) >>> >>> locale: >>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >>> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 >>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>> >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] biomaRt_2.8.0 DESeq_1.4.1 locfit_1.5-6 lattice_0.19-23 >>> [5] akima_0.5-4 Biobase_2.12.1 WriteXLS_2.1.0 gdata_2.8.2 >>> [9] limma_3.8.2 >>> >>> loaded via a namespace (and not attached): >>> [1] annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5 >>> [4] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0 >>> [7] gtools_2.6.2 RColorBrewer_1.0-2 RCurl_1.6-4 >>> [10] RSQLite_0.9-4 splines_2.13.0 survival_2.36-5 >>> [13] tools_2.13.0 XML_3.4-0 xtable_1.5-6 >>> >>> >>> Many Thanks, >>> Natasha >>> >>> -- >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- Natasha Sahgal, PhD Research Associate in Functional Genomics Bioinformatics& Statistical Genetics Core Wellcome Trust Center for Human Genetics University of Oxford Roosevelt Drive Oxford OX3 7BN U.K. Tel: + 44 -(0)1865 287 609 Fax: + 44 -(0)1865 287 664
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Natasha, On 11-08-18 09:54 AM, Natasha Sahgal wrote: > Dear Herve, > > Thanks for this. > > Though with "with_illumina_humanht_12" and "illumina_humanht_12" are > definitely in the filters. > > listMarts(host="www.ensembl.org") > ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", > dataset="hsapiens_gene_ensembl") > filt = listFilters(ensembl) > > filt[grep("illumina", filt[[1]], ignore.case=TRUE), ] > name description > 12 with_illumina_humanwg_6_v1 with Illumina HumanWG 6 v1 ID(s)) > 13 with_illumina_humanwg_6_v2 with Illumina HumanWG 6 v2 ID(s) > 14 with_illumina_humanwg_6_v3 with Illumina HumanWG 6 v3 ID(s) > 15 with_illumina_humanht_12 with Illumina Human HT 12 ID(s) > 125 illumina_humanwg_6_v1 Illumina HumanWG 6 V1 ID(s) [e.g. 0000940471] > 126 illumina_humanwg_6_v2 Illumina HumanWG 6 V2 ID(s) [e.g. ILMN_1748182] > 127 illumina_humanwg_6_v3 Illumina HumanWG 6 v3 ID(s) [e.g. ILMN_2103362] > 128 illumina_humanht_12 Illumina Human HT 12 ID(s) [e.g. ILMN_1672925] Ah, I was looking at the attributes, my bad. So it looks to me that the 1st filter is a boolean (TRUE/FALSE) that you can turn on in order to only retrieve genes that are associated with an Illumina Human HT 12 ID (i.e. any ID): > genes1 <- getBM(attributes="ensembl_gene_id", filters="with_illumina_humanht_12", values=TRUE, mart=ensembl) > dim(genes1) [1] 21719 1 With the 2nd filter you can actually specify the IDs that you are interested in: > genes2 <- getBM(attributes="ensembl_gene_id", filters="illumina_humanht_12", values="ILMN_167292", mart=ensembl) > dim(genes2) [1] 0 1 > genes2 [1] ensembl_gene_id <0 rows> (or 0-length row.names) Mmh it looks like there's no gene associated with the ID they give in the description of the filter (as an example). Trying with an other ID seems to work though: > genes2 <- getBM(attributes="ensembl_gene_id", filters="illumina_humanht_12", values="ILMN_2103362", mart=ensembl) > dim(genes2) [1] 1 1 > genes2 ensembl_gene_id 1 ENSG00000159314 Hope this helps, H. > > Many Thanks, > Natasha > > > On 18/08/2011 15:04, Hervé Pagès wrote: >> Natasha, >> >> On 11-08-18 06:32 AM, Natasha Sahgal wrote: >>> Dear All, >>> >>> Please ignore this, as now it does appear to work. I do wonder, why did >>> it not work earlier though. >>> >>> Also, could someone please tell me the difference between >>> "with_illumina_humanht_12" and "illumina_humanht_12" in the filters and >>> attributes? >> >> I don't see the "with_illumina_humanht_12" attribute: >> >> library(biomaRt) >> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", >> dataset="hsapiens_gene_ensembl") >> atts = listAttributes(ensembl) >> >> Then: >> >> > atts[grep("illumina", atts[[1]], ignore.case=TRUE), ] >> name description >> 104 illumina_humanwg_6_v1 Illumina HumanWG 6 v1 >> 105 illumina_humanwg_6_v2 Illumina HumanWG 6 v2 >> 106 illumina_humanwg_6_v3 Illumina HumanWG 6 v3 >> 107 illumina_humanht_12 Illumina Human HT 12 >> >>> What version of the illumina_humanht_12 chip is used, as this is >>> unclear? >> >> According to the Illumina website the latest version of this chip seems >> to be v4 but it's not clear indeed that the Emsembl folks are referring >> to that one. You might want to ask them directly (biomaRt is just a tool >> to query data their data). >> >> Cheers, >> H. >> >>> >>> >>> Many Thanks, >>> Natasha >>> >>> On 18/08/2011 11:02, Natasha Sahgal wrote: >>>> Dear List, >>>> >>>> I am using biomaRt for the first time. >>>> >>>> Initially I had problems connecting to hsapiens dataset, though I >>>> could listMarts. However that issue was resolved (by solutions in some >>>> earlier posts) by changing the host to www.ensembl.org. >>>> >>>> Now though I get the following error message when I try to execute the >>>> following command: >>>> >>>> >mg_eg.ens.t <- getBM(attributes = >>>> c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_sy mbol"), >>>> >>>> filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = >>>> ensembl) >>>> >>>> >>>> V1 >>>> 1 <head> >>>> 2 <link rel="Shortcut" icon="" href="/errors/ensembl_ico.png">>>> type=image/png /> >>>> 3 The Ensembl Genome Browser >>>> 4 <style type="text/css"> >>>> 5 >>>> body{color:#333333;background-color:#eaeeff;font- family:Arial,Helvetica,Sans-serif;font-size:14pt;margin:0;padding:0} >>>> >>>> >>>> 6 >>>> #masthead{color:#ffffff;background- color:#333366;width:100%;height:50px;padding:5px >>>> >>>> 0;font-size:1.75em;text-align:center;margin:auto} >>>> Error in getBM(attributes = c("entrezgene", "ensembl_gene_id", >>>> "ensembl_transcript_id", : >>>> The query to the BioMart webservice returned an invalid result: the >>>> number of columns in the result table does not equal the number of >>>> attributes in the query. Please report this to the mailing list. >>>> >>>> >>>> This I found strange as I did the same thing yesterday with another >>>> object and it worked!! >>>> >>>> Full Code and SessionInfo: >>>> >>>> headmg.u.eg$Entrez_Gene_ID) #[1] 27122 3488 72 1293 100134134 390 >>>> >>>> lengthmg.u.eg$Entrez_Gene_ID) #[1] 4288 >>>> >>>> >>>> listMarts(host="www.ensembl.org") >>>> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org") >>>> listDatasets(ensembl) >>>> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org", >>>> dataset="hsapiens_gene_ensembl") >>>> filt = listFilters(ensembl) >>>> atts = listAttributes(ensembl) >>>> >>>> mg_eg.ens <- getBM(attributes = >>>> c("entrezgene","ensembl_gene_id","hgnc_symbol"), filters = >>>> "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) # 4016 3 >>>> >>>> mg_eg.ens.t <- getBM(attributes = >>>> c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_sy mbol"), >>>> >>>> filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = >>>> ensembl) >>>> >>>> sessionInfo() >>>> R version 2.13.0 (2011-04-13) >>>> Platform: x86_64-pc-linux-gnu (64-bit) >>>> >>>> locale: >>>> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >>>> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >>>> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8 >>>> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >>>> [9] LC_ADDRESS=C LC_TELEPHONE=C >>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] stats graphics grDevices utils datasets methods base >>>> >>>> other attached packages: >>>> [1] biomaRt_2.8.0 DESeq_1.4.1 locfit_1.5-6 lattice_0.19-23 >>>> [5] akima_0.5-4 Biobase_2.12.1 WriteXLS_2.1.0 gdata_2.8.2 >>>> [9] limma_3.8.2 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5 >>>> [4] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0 >>>> [7] gtools_2.6.2 RColorBrewer_1.0-2 RCurl_1.6-4 >>>> [10] RSQLite_0.9-4 splines_2.13.0 survival_2.36-5 >>>> [13] tools_2.13.0 XML_3.4-0 xtable_1.5-6 >>>> >>>> >>>> Many Thanks, >>>> Natasha >>>> >>>> -- >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
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