biomaRt query problems- plants_mart_10
1
0
Entering edit mode
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
ADD COMMENT •
0
Entering edit mode
@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
ADD COMMENT •
0
Entering edit mode
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 >
ADD REPLY •
0
Entering edit mode
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
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 1072 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6