makeTranscriptDbFromBiomart for Arabidopsis thaliana (plants_mart_10)

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annaick.carles ▴ 20

@annaickcarles-4868

Last seen 10.4 years ago

Dear Bioconductor mailing list, i need to get the length of genes in Arabidopsis thaliana in order to use the R package 'goseq'. Since Arabidopsis thaliana is not in the native 'goseq' database, I first tried to get a 'transcriptDb' object as suggested in the documentation of 'goseq', with 'makeTranscriptDbFromBiomart' command from the 'GenomicFeatures' package. But I got the following error message: ----------------------------------- > txdb_At<-makeTranscriptDbFromBiomart(biomart="plants_mart_10",dataset= "athaliana_eg_gene") Download and preprocess the 'transcripts' data frame ... V1 1 2 <html><head><meta http-equiv="Content-Type" content="text/html;" charset="iso-8859-1"> 3 <title>ERROR: The requested URL could not be retrieved</title> 4 <style type="text/css"></style> 5 </head><body> 6

ERROR

Error in getBM(.A1_ATTRIBS, filters = filters, values = values, mart = mart) : 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: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C [5] LC_TIME=English_United Kingdom.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] org.At.tair.db_2.5.0 RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.14.1 Biobase_2.12.2 goseq_1.4.0 geneLenDataBase_0.99.7 BiasedUrn_1.04 [9] biomaRt_2.8.1 GenomicFeatures_1.4.4 GenomicRanges_1.4.8 IRanges_1.10.6 rtracklayer_1.12.4 RCurl_1.6-10.1 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biostrings_2.20.3 BSgenome_1.20.0 grid_2.13.0 lattice_0.19-33 Matrix_0.9996875-3 mgcv_1.7-6 nlme_3.1-102 tools_2.13.0 XML_3.4-2.2 > ----------------------------------- Many thanks in advance for your help! Annaick Carles FRISYS Core Facility Data Management ZBSA - University of Freiburg Germany

Arabidopsis thaliana biomaRt Arabidopsis thaliana biomaRt • 1.6k views

ADD COMMENT • link 13.4 years ago annaick.carles ▴ 20

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Marc Carlson ★ 7.2k

@marc-carlson-2264

Last seen 8.5 years ago

United States

Hi Annaick, I was unable to reproduce your error. My sessionInfo() (below), shows a very similar result to yours (only R looks different which is unlikely to cause this). But biomaRt sometimes can be a little testy since it relies on a web-service. So perhaps you should try again? Marc > sessionInfo() R version 2.13.1 Patched (2011-08-25 r56798) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.4.4 GenomicRanges_1.4.8 IRanges_1.10.6 loaded via a namespace (and not attached): [1] biomaRt_2.8.1 Biostrings_2.20.3 BSgenome_1.20.0 DBI_0.2-5 [5] RCurl_1.6-9 RSQLite_0.9-4 rtracklayer_1.12.4 tools_2.13.1 [9] XML_3.4-2 Marc On 09/20/2011 03:08 AM, annaick.carles wrote: > Dear Bioconductor mailing list, > > i need to get the length of genes in Arabidopsis thaliana in order to > use the R package 'goseq'. Since Arabidopsis thaliana is not in the > native 'goseq' database, I first tried to get a 'transcriptDb' object > as suggested in the documentation of 'goseq', with > 'makeTranscriptDbFromBiomart' command from the 'GenomicFeatures' > package. But I got the following error message: > > ----------------------------------- > > > txdb_At<-makeTranscriptDbFromBiomart(biomart="plants_mart_10",datase t="athaliana_eg_gene") > Download and preprocess the 'transcripts' data frame ... > V1 > 1 http://www.w3.org/TR/html4/loose.dtd> > 2 <html><head><meta http-equiv="Content-Type" content="text/html;"> charset=iso-8859-1> > 3 ERROR: The requested URL could not be retrieved > 4 <style> type=text/css></style> > 5 </head><body> > 6

ERROR

> Error in getBM(.A1_ATTRIBS, filters = filters, values = values, mart = > mart) : > 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: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C > [5] LC_TIME=English_United Kingdom.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] org.At.tair.db_2.5.0 RSQLite_0.9-4 DBI_0.2-5 > AnnotationDbi_1.14.1 Biobase_2.12.2 goseq_1.4.0 > geneLenDataBase_0.99.7 BiasedUrn_1.04 > [9] biomaRt_2.8.1 GenomicFeatures_1.4.4 GenomicRanges_1.4.8 > IRanges_1.10.6 rtracklayer_1.12.4 RCurl_1.6-10.1 > bitops_1.0-4.1 > > loaded via a namespace (and not attached): > [1] Biostrings_2.20.3 BSgenome_1.20.0 grid_2.13.0 lattice_0.19-33 > Matrix_0.9996875-3 mgcv_1.7-6 nlme_3.1-102 tools_2.13.0 > XML_3.4-2.2 > > > ----------------------------------- > > > Many thanks in advance for your help! > > > Annaick Carles > FRISYS Core Facility Data Management > ZBSA - University of Freiburg > Germany > > _______________________________________________ > 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 COMMENT • link 13.4 years ago Marc Carlson ★ 7.2k

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annaick.carles ▴ 20

@annaickcarles-4868

Last seen 10.4 years ago

Hi Marc, many thanks for your fast reply. I managed to make it working by using another machine which has direct access to the internet (not via proxy). --------------------------------------------- > txdb_At<-makeTranscriptDbFromBiomart(biomart="plants_mart_10",dataset= "athaliana_eg_gene") Download and preprocess the 'transcripts' data frame ... OK Download and preprocess the 'splicings' data frame ... OK Download and preprocess the 'genes' data frame ... OK Prepare the 'metadata' data frame ... OK Make the TranscriptDb object ... OK Warning messages: 1: In .normargSplicings(splicings, unique_tx_ids) : no CDS information for this TranscriptDb object 2: In .normargChrominfo(chrominfo, transcripts$tx_chrom, splicings$exon_chrom) : chromosome lengths and circularity flags are not available for this TranscriptDb object > > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.2.3 GenomicRanges_1.2.3 IRanges_1.8.9 [4] biomaRt_2.6.0 RCurl_1.6-10 bitops_1.0-4.1 loaded via a namespace (and not attached): [1] Biobase_2.10.0 Biostrings_2.18.4 BSgenome_1.18.3 DBI_0.2-5 [5] RSQLite_0.9-4 rtracklayer_1.10.6 tools_2.12.0 XML_3.4-0 > --------------------------------------------- Best, Annaick --- Hi Annaick, I was unable to reproduce your error. My sessionInfo() (below), shows a very similar result to yours (only R looks different which is unlikely to cause this). But biomaRt sometimes can be a little testy since it relies on a web-service. So perhaps you should try again? Marc > sessionInfo() R version 2.13.1 Patched (2011-08-25 r56798) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.4.4 GenomicRanges_1.4.8 IRanges_1.10.6 loaded via a namespace (and not attached): [1] biomaRt_2.8.1 Biostrings_2.20.3 BSgenome_1.20.0 DBI_0.2-5 [5] RCurl_1.6-9 RSQLite_0.9-4 rtracklayer_1.12.4 tools_2.13.1 [9] XML_3.4-2 Marc On 09/20/2011 03:08 AM, annaick.carles wrote: > > Dear Bioconductor mailing list, > > > > i need to get the length of genes in Arabidopsis thaliana in order to > > use the R package 'goseq'. Since Arabidopsis thaliana is not in the > > native 'goseq' database, I first tried to get a 'transcriptDb' object > > as suggested in the documentation of 'goseq', with > > 'makeTranscriptDbFromBiomart' command from the 'GenomicFeatures' > > package. But I got the following error message: > > > > ----------------------------------- >> > > > > txdb_At<-makeTranscriptDbFromBiomart(biomart="plants_mart_10",dataset= "athaliana_eg_gene") > > Download and preprocess the 'transcripts' data frame ... > > V1 > > 1 > http://www.w3.org/TR/html4/loose.dtd> > > 2 <html><head><meta http-equiv="Content-Type" content="text/html;"> > charset=iso-8859-1> > > 3 ERROR: The requested URL could not be retrieved > > 4 <style> > type=text/css></style> > > 5 </head><body> > > 6

ERROR

> > Error in getBM(.A1_ATTRIBS, filters = filters, values = values, mart = > > mart) : > > 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: i386-pc-mingw32/i386 (32-bit) > > > > locale: > > [1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United > > Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United Kingdom.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] org.At.tair.db_2.5.0 RSQLite_0.9-4 DBI_0.2-5 > > AnnotationDbi_1.14.1 Biobase_2.12.2 goseq_1.4.0 > > geneLenDataBase_0.99.7 BiasedUrn_1.04 > > [9] biomaRt_2.8.1 GenomicFeatures_1.4.4 GenomicRanges_1.4.8 > > IRanges_1.10.6 rtracklayer_1.12.4 RCurl_1.6-10.1 > > bitops_1.0-4.1 > > > > loaded via a namespace (and not attached): > > [1] Biostrings_2.20.3 BSgenome_1.20.0 grid_2.13.0 lattice_0.19-33 > > Matrix_0.9996875-3 mgcv_1.7-6 nlme_3.1-102 tools_2.13.0 > > XML_3.4-2.2 >> > > > > ----------------------------------- > > > > > > Many thanks in advance for your help! > > > > > > Annaick Carles

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