[BioC] BiomaRt Query error Edited

Sat Jun 9 02:10:39 CEST 2012

Hi Avoks,

Could you maybe give us a few genes that cause the error for you?  We 
don't have your file, so we have no idea what that read.delim call will 
put into 'genes'.

   Marc

On 06/05/2012 04:56 AM, Ovokeraye Achinike-Oduaran wrote:
> My apologies. I omitted the "error" in my initial post.
>
> Hi all,
>
> I ran a list of genes through biomaRt with the following code and it
> gives me this error in the snp retrieval aspect of it. I doubt it's a
> connection/proxy problem because I have that taken care of, I think
> and every step prior to that seemed to have worked just fine.
>
> Any ideas what the problem might be?
>
> Thanks.
>
> -Avoks
>
> mart = useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
> genes = read.delim("DAVID_BFE_Genes_4_06_2012.txt", header = TRUE)
> results = getBM(attributes = c("ensembl_gene_id", "hgnc_symbol",
> "chromosome_name","strand", "transcript_start", "transcript_end" ),
> filters = "hgnc_symbol", values = genes$Symbol, mart = mart)
> mart2 = useMart(biomart="snp", dataset="hsapiens_snp")
> results2 = getBM(attributes = c("refsnp_id", "allele", "snp",
>         "chrom_strand", "cds_start","cds_end","validated",
>         "consequence_type_tv","phenotype_name"),
>         filters = "ensembl_gene", values = results$ensembl_gene_id, mart = mart2)
>
> <!DOCTYPE HTML PUBLIC -//W3C//DTD HTML 4.01 Transitional//EN
> http://www.w3.org/TR/html4/loose.dtd>
> 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><!--BODY{background-color:#ffffff;font-family:verdana,sans-serif}PRE{font-family:sans-serif}--></STYLE>
> 5
>                                            </HEAD><BODY>
> 6
>                                           <H1>ERROR</H1>
> Error in getBM(attributes = c("refsnp_id", "allele", "snp", "chrom_strand",  :
>    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 2.15.0 (2012-03-30)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_1252  LC_CTYPE=English_.1252
> [3] LC_MONETARY=English_.1252 LC_NUMERIC=C
> [5] LC_TIME=English_.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] BiocInstaller_1.4.6 biomaRt_2.12.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.91-1.1 tools_2.15.0   XML_3.9-4.1
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