refseq to genesymbol with BiomaRt - problem occurs
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Andrea Grilli ▴ 240
@andrea-grilli-4664
Last seen 8.8 years ago
Italy, Bologna, Rizzoli Orthopaedic Ins…
Dear list, I need to convert refseq ID to genesymbol. I used biomaRt but I get this error: > library(biomaRt) > mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") > getGene(id = "NM_053017", type = "refseq_mrna", mart = mart) V1 1 2 <html><head><meta http-equiv="Content-Type" content="text/html;" charset="iso-8859-1"> 3 <title>ERRORE: La URL richiesta non può essere recuperata</title> 4 <style type="text/css"></style> 5 </head><body> 6

ERRORE

Error in getBM(attributes = attrib, filters = type, values = id, 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. In fact I need to process a vector of refseq id with the following code but I get same error as before: > getGene(id = table[,1], type = "refseq_mrna", mart = mart) Changing the id type (e.g. refseq_dna) doesn't change the result. Is it my input error or some problem with biomaRt package occurred? Thanks in advance, Andrea > sessionInfo() R version 2.14.0 (2011-10-31) Platform: i686-pc-linux-gnu (32-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C 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] annotate_1.32.0 biomaRt_2.10.0 annaffy_1.26.0 [4] KEGG.db_2.6.1 GO.db_2.6.1 hgu133plus2.db_2.6.3 [7] org.Hs.eg.db_2.6.4 RSQLite_0.11.1 DBI_0.2-5 [10] AnnotationDbi_1.16.10 Biobase_2.14.0 loaded via a namespace (and not attached): [1] IRanges_1.12.5 RCurl_1.8-0 tools_2.14.0 XML_3.6-2 xtable_1.6-0
GO hgu133plus2 PROcess convert biomaRt GO hgu133plus2 PROcess convert biomaRt • 1.3k views
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@wolfgang-huber-3550
Last seen 3 months ago
EMBL European Molecular Biology Laborat…
Dear Andrea the same query just worked fine for me (see below), perhaps it is a problem with your internet connection (see also the error message that you received)? Best wishes Wolfgang library(biomaRt) mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") getGene(id = "NM_053017", type = "refseq_mrna", mart = mart) refseq_mrna hgnc_symbol 1 NM_053017 ART5 description chromosome_name band 1 ADP-ribosyltransferase 5 [Source:HGNC Symbol;Acc:24049] 11 p15.4 strand start_position end_position ensembl_gene_id 1 -1 3659733 3663546 ENSG00000167311 On 1/31/12 11:05 AM, andrea.grilli at ior.it wrote: > > Dear list, > I need to convert refseq ID to genesymbol. I used biomaRt but I get this > error: > >> library(biomaRt) >> mart = useMart("ensembl", dataset="hsapiens_gene_ensembl") >> getGene(id = "NM_053017", type = "refseq_mrna", mart = mart) > 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 ERRORE: La URL richiesta non può essere recuperata > 4 <style> type=text/css></style> > > 5 </head><body> > 6

ERRORE

> Error in getBM(attributes = attrib, filters = type, values = id, 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. > > In fact I need to process a vector of refseq id with the following code > but I get same error as before: >> getGene(id = table[,1], type = "refseq_mrna", mart = mart) > > Changing the id type (e.g. refseq_dna) doesn't change the result. Is it > my input error or some problem with biomaRt package occurred? > Thanks in advance, > Andrea > > > > >> sessionInfo() > R version 2.14.0 (2011-10-31) > Platform: i686-pc-linux-gnu (32-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=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C 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] annotate_1.32.0 biomaRt_2.10.0 annaffy_1.26.0 > [4] KEGG.db_2.6.1 GO.db_2.6.1 hgu133plus2.db_2.6.3 > [7] org.Hs.eg.db_2.6.4 RSQLite_0.11.1 DBI_0.2-5 > [10] AnnotationDbi_1.16.10 Biobase_2.14.0 > > loaded via a namespace (and not attached): > [1] IRanges_1.12.5 RCurl_1.8-0 tools_2.14.0 XML_3.6-2 xtable_1.6-0 > > _______________________________________________ > 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 -- Best wishes Wolfgang Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber
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