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
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
