biomaRt query problems- plants_mart_10
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Samuel Wuest ▴ 330
@samuel-wuest-2821
Last seen 10.3 years ago
Hi, I have tried to use biomaRt (primarily for use in the GenomeGraphs-package) to retrieve data from the pants_mart_10 -Mart, and it seems that the service is unstable at the moment (that is, it works in times but not others). I observed the problem firstly two days ago and I have not been able to connect today... Below, I have included some example code to demonstrate the error. I have read a similar post on the topic, where the problems seemed to have been at the server-side and not the user-side (?). Any suggestions, in case I have to troubleshoot on my side? Thanks a lot for any help. Best, Sam > library(org.At.tair.db) > library(biomaRt) > > myMart <- useMart("plants_mart_10", dataset="athaliana_eg_gene") > > genes <- ls(org.At.tairSYMBOL)[1:10] > att <- listAttributes(myMart)[1:5,1] > filt <- "tair_locus" > > retr.data <- getBM(att, filt, values=genes, myMart) V1 1 2 <html xmlns="&lt;a href=" http:="" www.w3.org="" 1999="" xhtml"="" rel="nofollow">http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> 3 <head> 4 Information Systems Services - Trinity College Dublin - Access error 503 5 <meta http-equiv="Content-Type" content="text/html;" charset="iso-8859-1"/> 6 <meta name="keywords" content="trinity" college="" dublin,="" trinity,="" university="" of="" dublin,="" university,="" ireland=""/> Error in getBM(att, filt, values = genes, myMart) : 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. > > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.8.0 org.At.tair.db_2.5.0 RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.14.1 Biobase_2.12.1 loaded via a namespace (and not attached): [1] RCurl_1.5-0 XML_3.4-0 ------------------------------------------------------- Samuel Wuest Smurfit Institute of Genetics Trinity College Dublin Dublin 2, Ireland Phone: +353-1-896 2444 Web: http://www.tcd.ie/Genetics/wellmer-2/index.html Email: wuests at tcd.ie
biomaRt biomaRt • 1.3k views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear Sam I have just run your script, and it seemed to work fine. Session info and output are below. Looking at your error message: "Information Systems Services - Trinity College Dublin - Access error 503" it does look like a problem with your local configuration at TCD. Best wishes Wolfgang > str(retr.data) 'data.frame': 21 obs. of 5 variables: $ ensembl_gene_id : chr "AT1G01060" "AT1G01060" ... $ ensembl_transcript_id : chr "AT1G01060.3" "AT1G01060.5" ... $ ensembl_peptide_id : chr "AT1G01060.3" "AT1G01060.5" ... $ canonical_transcript_stable_id: chr "AT1G01060.3" "AT1G01060.3" ... $ description : chr "Homeodomain-like superfamily protein.[Source:TAIR;Acc:AT1G01060]" ... > sessionInfo() R Under development (unstable) (2011-10-23 r57407) Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] biomaRt_2.9.3 org.At.tair.db_2.6.4 RSQLite_0.10.0 [4] DBI_0.2-5 AnnotationDbi_1.15.40 Biobase_2.13.11 [7] BiocInstaller_1.1.29 fortunes_1.4-2 loaded via a namespace (and not attached): [1] IRanges_1.11.31 RCurl_1.6-10 XML_3.4-3 tools_2.15.0 Oct/22/11 2:34 PM, Samuel Wuest scripsit:: > Hi, > > I have tried to use biomaRt (primarily for use in the > GenomeGraphs-package) to retrieve data from the pants_mart_10 -Mart, > and it seems that the service is unstable at the moment (that is, it > works in times but not others). I observed the problem firstly two > days ago and I have not been able to connect today... > > Below, I have included some example code to demonstrate the error. I > have read a similar post on the topic, where the problems seemed to > have been at the server-side and not the user-side (?). > > Any suggestions, in case I have to troubleshoot on my side? > > Thanks a lot for any help. > > Best, Sam > > >> library(org.At.tair.db) >> library(biomaRt) >> >> myMart<- useMart("plants_mart_10", dataset="athaliana_eg_gene") >> >> genes<- ls(org.At.tairSYMBOL)[1:10] >> att<- listAttributes(myMart)[1:5,1] >> filt<- "tair_locus" >> >> retr.data<- getBM(att, filt, values=genes, myMart) > > V1 > 1 http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd> > 2<html> xmlns=http://www.w3.org/1999/xhtml xml:lang=en lang=en> > 3 > <head> > 4Information Systems Services - > Trinity College Dublin - Access error 503 > 5<meta> http-equiv=Content-Type content=text/html; charset=iso-8859-1 /> > 6<meta name="keywords" content="trinity" college="" dublin,=""> trinity, university of dublin, university, ireland /> > Error in getBM(att, filt, values = genes, myMart) : > 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. >> >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] biomaRt_2.8.0 org.At.tair.db_2.5.0 RSQLite_0.9-4 > DBI_0.2-5 AnnotationDbi_1.14.1 Biobase_2.12.1 > > loaded via a namespace (and not attached): > [1] RCurl_1.5-0 XML_3.4-0 > > ------------------------------------------------------- > Samuel Wuest > Smurfit Institute of Genetics > Trinity College Dublin > Dublin 2, Ireland > Phone: +353-1-896 2444 > Web: http://www.tcd.ie/Genetics/wellmer-2/index.html > Email: wuests at tcd.ie > > _______________________________________________ > 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 -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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On Sun, Oct 23, 2011 at 2:27 PM, Wolfgang Huber <whuber at="" embl.de=""> wrote: > Dear Sam > > I have just run your script, and it seemed to work fine. Session info and > output are below. > > Looking at your error message: "Information Systems Services - Trinity > College Dublin - Access error 503" it does look like a problem with your > local configuration at TCD. > It could also be the scheduled downtime for the biomart servers, please see the announcement here: https://stat.ethz.ch/pipermail/bioconductor/2011-October/041685.html Dan > ? ? ? ?Best wishes > ? ? ? ?Wolfgang > >> str(retr.data) > 'data.frame': ? 21 obs. of ?5 variables: > ?$ ensembl_gene_id ? ? ? ? ? ? ? : chr ?"AT1G01060" "AT1G01060" ... > ?$ ensembl_transcript_id ? ? ? ? : chr ?"AT1G01060.3" "AT1G01060.5" ... > ?$ ensembl_peptide_id ? ? ? ? ? ?: chr ?"AT1G01060.3" "AT1G01060.5" ... > ?$ canonical_transcript_stable_id: chr ?"AT1G01060.3" "AT1G01060.3" ... > ?$ description ? ? ? ? ? ? ? ? ? : chr ?"Homeodomain-like superfamily > protein.[Source:TAIR;Acc:AT1G01060]" ... > >> sessionInfo() > R Under development (unstable) (2011-10-23 r57407) > Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] biomaRt_2.9.3 ? ? ? ? org.At.tair.db_2.6.4 ?RSQLite_0.10.0 > [4] DBI_0.2-5 ? ? ? ? ? ? AnnotationDbi_1.15.40 Biobase_2.13.11 > [7] BiocInstaller_1.1.29 ?fortunes_1.4-2 > > loaded via a namespace (and not attached): > [1] IRanges_1.11.31 RCurl_1.6-10 ? ?XML_3.4-3 ? ? ? tools_2.15.0 > > > > Oct/22/11 2:34 PM, Samuel Wuest scripsit:: >> >> Hi, >> >> I have tried to use biomaRt (primarily for use in the >> GenomeGraphs-package) to retrieve data from the pants_mart_10 -Mart, >> and it seems that the service is unstable at the moment (that is, it >> works in times but not others). I observed the problem firstly two >> days ago and I have not been able to connect today... >> >> Below, I have included some example code to demonstrate the error. I >> have read a similar post on the topic, where the problems seemed to >> have been at the server-side and not the user-side (?). >> >> Any suggestions, in case I have to troubleshoot on my side? >> >> Thanks a lot for any help. >> >> Best, Sam >> >> >>> library(org.At.tair.db) >>> library(biomaRt) >>> >>> myMart<- useMart("plants_mart_10", dataset="athaliana_eg_gene") >>> >>> genes<- ls(org.At.tairSYMBOL)[1:10] >>> att<- listAttributes(myMart)[1:5,1] >>> filt<- "tair_locus" >>> >>> retr.data<- getBM(att, filt, values=genes, myMart) >> >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? V1 >> 1> http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd> >> 2<html>> xmlns=http://www.w3.org/1999/xhtml xml:lang=en lang=en> >> 3 >> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <head> >> 4Information Systems Services - >> Trinity College Dublin - Access error 503 >> 5<meta>> http-equiv=Content-Type content=text/html; charset=iso-8859-1 /> >> 6<meta name="keywords" content="trinity" college="" dublin,="">> trinity, university of dublin, university, ireland /> >> Error in getBM(att, filt, values = genes, myMart) : >> ? 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. >>> >>> sessionInfo() >> >> R version 2.13.0 (2011-04-13) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8 >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] biomaRt_2.8.0 ? ? ? ?org.At.tair.db_2.5.0 RSQLite_0.9-4 >> DBI_0.2-5 ? ? ? ? ? ?AnnotationDbi_1.14.1 Biobase_2.12.1 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.5-0 XML_3.4-0 >> >> ------------------------------------------------------- >> Samuel Wuest >> Smurfit Institute of Genetics >> Trinity College Dublin >> Dublin 2, Ireland >> Phone: +353-1-896 2444 >> Web: http://www.tcd.ie/Genetics/wellmer-2/index.html >> Email: wuests at tcd.ie >> >> _______________________________________________ >> 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 > > > -- > > > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > 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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Oh, I am sorry, haven't seen the announcement. My queries are working again, so back to normal. Thanks a lot! Sam On 23 October 2011 22:32, Dan Tenenbaum <dtenenba at="" fhcrc.org=""> wrote: > On Sun, Oct 23, 2011 at 2:27 PM, Wolfgang Huber <whuber at="" embl.de=""> wrote: >> Dear Sam >> >> I have just run your script, and it seemed to work fine. Session info and >> output are below. >> >> Looking at your error message: "Information Systems Services - Trinity >> College Dublin - Access error 503" it does look like a problem with your >> local configuration at TCD. >> > > It could also be the scheduled downtime for the biomart servers, > please see the announcement here: > > https://stat.ethz.ch/pipermail/bioconductor/2011-October/041685.html > > Dan > > >> ? ? ? ?Best wishes >> ? ? ? ?Wolfgang >> >>> str(retr.data) >> 'data.frame': ? 21 obs. of ?5 variables: >> ?$ ensembl_gene_id ? ? ? ? ? ? ? : chr ?"AT1G01060" "AT1G01060" ... >> ?$ ensembl_transcript_id ? ? ? ? : chr ?"AT1G01060.3" "AT1G01060.5" ... >> ?$ ensembl_peptide_id ? ? ? ? ? ?: chr ?"AT1G01060.3" "AT1G01060.5" ... >> ?$ canonical_transcript_stable_id: chr ?"AT1G01060.3" "AT1G01060.3" ... >> ?$ description ? ? ? ? ? ? ? ? ? : chr ?"Homeodomain-like superfamily >> protein.[Source:TAIR;Acc:AT1G01060]" ... >> >>> sessionInfo() >> R Under development (unstable) (2011-10-23 r57407) >> Platform: x86_64-apple-darwin10.8.0/x86_64 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] biomaRt_2.9.3 ? ? ? ? org.At.tair.db_2.6.4 ?RSQLite_0.10.0 >> [4] DBI_0.2-5 ? ? ? ? ? ? AnnotationDbi_1.15.40 Biobase_2.13.11 >> [7] BiocInstaller_1.1.29 ?fortunes_1.4-2 >> >> loaded via a namespace (and not attached): >> [1] IRanges_1.11.31 RCurl_1.6-10 ? ?XML_3.4-3 ? ? ? tools_2.15.0 >> >> >> >> Oct/22/11 2:34 PM, Samuel Wuest scripsit:: >>> >>> Hi, >>> >>> I have tried to use biomaRt (primarily for use in the >>> GenomeGraphs-package) to retrieve data from the pants_mart_10 -Mart, >>> and it seems that the service is unstable at the moment (that is, it >>> works in times but not others). I observed the problem firstly two >>> days ago and I have not been able to connect today... >>> >>> Below, I have included some example code to demonstrate the error. I >>> have read a similar post on the topic, where the problems seemed to >>> have been at the server-side and not the user-side (?). >>> >>> Any suggestions, in case I have to troubleshoot on my side? >>> >>> Thanks a lot for any help. >>> >>> Best, Sam >>> >>> >>>> library(org.At.tair.db) >>>> library(biomaRt) >>>> >>>> myMart<- useMart("plants_mart_10", dataset="athaliana_eg_gene") >>>> >>>> genes<- ls(org.At.tairSYMBOL)[1:10] >>>> att<- listAttributes(myMart)[1:5,1] >>>> filt<- "tair_locus" >>>> >>>> retr.data<- getBM(att, filt, values=genes, myMart) >>> >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? V1 >>> 1>> http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd> >>> 2<html>>> xmlns=http://www.w3.org/1999/xhtml xml:lang=en lang=en> >>> 3 >>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? <head> >>> 4Information Systems Services - >>> Trinity College Dublin - Access error 503 >>> 5<meta>>> http-equiv=Content-Type content=text/html; charset=iso-8859-1 /> >>> 6<meta name="keywords" content="trinity" college="" dublin,="">>> trinity, university of dublin, university, ireland /> >>> Error in getBM(att, filt, values = genes, myMart) : >>> ? 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. >>>> >>>> sessionInfo() >>> >>> R version 2.13.0 (2011-04-13) >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>> >>> locale: >>> [1] en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8 >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> other attached packages: >>> [1] biomaRt_2.8.0 ? ? ? ?org.At.tair.db_2.5.0 RSQLite_0.9-4 >>> DBI_0.2-5 ? ? ? ? ? ?AnnotationDbi_1.14.1 Biobase_2.12.1 >>> >>> loaded via a namespace (and not attached): >>> [1] RCurl_1.5-0 XML_3.4-0 >>> >>> ------------------------------------------------------- >>> Samuel Wuest >>> Smurfit Institute of Genetics >>> Trinity College Dublin >>> Dublin 2, Ireland >>> Phone: +353-1-896 2444 >>> Web: http://www.tcd.ie/Genetics/wellmer-2/index.html >>> Email: wuests at tcd.ie >>> >>> _______________________________________________ >>> 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 >> >> >> -- >> >> >> Wolfgang Huber >> EMBL >> http://www.embl.de/research/units/genome_biology/huber >> >> _______________________________________________ >> 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 > > -- ----------------------------------------------------- Samuel Wuest Smurfit Institute of Genetics Trinity College Dublin Dublin 2, Ireland Phone: +353-1-896 2444 Web: http://www.tcd.ie/Genetics/wellmer-2/index.html Email: wuests at tcd.ie
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