chris_utah | 23 Jan 17:13 2013
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biomaRt error

Hi,

I am reporting a biomaRt error noted during some work.  The code did not return the flanking sequences of a SNP.

> getBM(attributes=c('refsnp_id', 'chr_name', 'chrom_start', 'allele', 'c57bl_6j', 'cast_eij',
'upstream_flank','downstream_flank'), filters=c("snp_filter"), values=( "rs6171921" ), mart = snpmart)->sps
  Variation Name Chromosome name Position on Chromosome (bp) Variant Alleles C57BL/6J CAST/EiJ
1      rs6171921               2                   157329549             G/A        G        A
Error in getBM(attributes = c("refsnp_id", "chr_name", "chrom_start",  : 
  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 2.15.2 (2012-10-26)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.14.0

loaded via a namespace (and not attached):
 [1] annotate_1.36.0      AnnotationDbi_1.20.2 Biobase_2.18.0       BiocGenerics_0.4.0   DBI_0.2-5           
DESeq_1.10.1        
 [7] genefilter_1.40.0    geneplotter_1.36.0   grid_2.15.2          IRanges_1.16.4       lattice_0.20-10     
parallel_2.15.2     
[13] RColorBrewer_1.0-5   RCurl_1.95-3         RSQLite_0.11.2       splines_2.15.2       stats4_2.15.2       
survival_2.36-14    
[19] XML_3.95-0.1         xtable_1.7-0        

Thank you.

best wishes,
Chris

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