refseq to genesymbol with BiomaRt - problem occurs
1
0
Entering edit mode
Andrea Grilli ▴ 240
@andrea-grilli-4664
Last seen 7.3 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 • 1.0k views
ADD COMMENT
0
Entering edit mode
@wolfgang-huber-3550
Last seen 17 days 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
ADD COMMENT

Login before adding your answer.

Traffic: 479 users visited in the last hour
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