[BioC] biomart error

Thu Aug 18 15:32:55 CEST 2011

Dear All,

Please ignore this, as now it does appear to work.  I do wonder, why did 
it not work earlier though.

Also, could someone please tell me the difference between 
"with_illumina_humanht_12" and "illumina_humanht_12" in the filters and 
attributes?

What version of the illumina_humanht_12 chip is used, as this is unclear?

Many Thanks,
Natasha

On 18/08/2011 11:02, 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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