[BioC] biomart error

Thu Aug 18 15:34:27 CEST 2011

Hi Natasha,

Not sure that is actually the cause of your problem but
you might want to update your installation to use the latest
versions of packages (e.g. your RCurl and biomaRt are not
the latest).

Instructions on how to update are here:

   http://bioconductor.org/install/

The problem might be something else but it doesn't hurt to keep
your installation up-to-date, all the contrary.

Cheers,
H.

On 11-08-18 03:02 AM, Natasha Sahgal wrote:
> Dear List,
>
> I am using biomaRt for the first time.
>
> Initially I had problems connecting to hsapiens dataset, though I could
> listMarts. However that issue was resolved (by solutions in some earlier
> posts) by changing the host to www.ensembl.org.
>
> Now though I get the following error message when I try to execute the
> following command:
>
>  >mg_eg.ens.t <- getBM(attributes =
> c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbol"),
> filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl)
>
>
> V1
> 1 <head>
> 2 <link rel=Shortcut Icon href=/errors/ensembl_ico.png type=image/png />
> 3 <title>The Ensembl Genome Browser</title>
> 4 <style type=text/css>
> 5
> body{color:#333333;background-color:#eaeeff;font-family:Arial,Helvetica,Sans-serif;font-size:14pt;margin:0;padding:0}
>
> 6
> #masthead{color:#ffffff;background-color:#333366;width:100%;height:50px;padding:5px
> 0;font-size:1.75em;text-align:center;margin:auto}
> Error in getBM(attributes = c("entrezgene", "ensembl_gene_id",
> "ensembl_transcript_id", :
> The query to the BioMart webservice returned an invalid result: the
> number of columns in the result table does not equal the number of
> attributes in the query. Please report this to the mailing list.
>
>
> This I found strange as I did the same thing yesterday with another
> object and it worked!!
>
> Full Code and SessionInfo:
>
> head(mg.u.eg$Entrez_Gene_ID) #[1] 27122 3488 72 1293 100134134 390
>
> length(mg.u.eg$Entrez_Gene_ID) #[1] 4288
>
>
> listMarts(host="www.ensembl.org")
> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
> listDatasets(ensembl)
> ensembl = useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org",
> dataset="hsapiens_gene_ensembl")
> filt = listFilters(ensembl)
> atts = listAttributes(ensembl)
>
> mg_eg.ens <- getBM(attributes =
> c("entrezgene","ensembl_gene_id","hgnc_symbol"), filters = "entrezgene",
> values = mg.u.eg$Entrez_Gene_ID, mart = ensembl) # 4016 3
>
> mg_eg.ens.t <- getBM(attributes =
> c("entrezgene","ensembl_gene_id","ensembl_transcript_id","hgnc_symbol"),
> filters = "entrezgene", values = mg.u.eg$Entrez_Gene_ID, mart = ensembl)
>
> sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8
> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] biomaRt_2.8.0 DESeq_1.4.1 locfit_1.5-6 lattice_0.19-23
> [5] akima_0.5-4 Biobase_2.12.1 WriteXLS_2.1.0 gdata_2.8.2
> [9] limma_3.8.2
>
> loaded via a namespace (and not attached):
> [1] annotate_1.30.0 AnnotationDbi_1.14.1 DBI_0.2-5
> [4] genefilter_1.34.0 geneplotter_1.30.0 grid_2.13.0
> [7] gtools_2.6.2 RColorBrewer_1.0-2 RCurl_1.6-4
> [10] RSQLite_0.9-4 splines_2.13.0 survival_2.36-5
> [13] tools_2.13.0 XML_3.4-0 xtable_1.5-6
>
>
> Many Thanks,
> Natasha
>
> --
>
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-- 
Hervé Pagès

Program in Computational Biology
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