[BioC] error with accessing biomaRt attributes

[Chao-Jen Wong]

Hi, Kishor,

How did you generate the object 'ensembl'? Can you double check to see
whether it is a valid, non-empty biomaRt object?

Kishor Tappita wrote:
> Dear List,
>
> I get the below error while trying to access biomaRt attributes.
>
>
>   
>> getBM(attributes = c("entrezgene"),values = c("202763_at","209310_s_at"),mart =ensembl)
>>     
> Error in getBM(attributes = c("entrezgene"), values = c("202763_at",
> "209310_s_at"),  :
> The query to the BioMart webservice returned an invalid result:
> biomaRt expected a character string of length 1. Please report this to
> the mailing list.
>
>
>   
>> sessionInfo()
>>     
> R version 2.9.2 (2009-08-24)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] RCurl_0.98-1        bitops_1.0-4.1      gene2pathway_1.2.0
> org.Dm.eg.db_2.2.11 RBGL_1.20.0         graph_1.22.2
> KEGGSOAP_1.18.0
>  [8] biomaRt_2.0.0       KEGG.db_2.2.11      RSQLite_0.7-2
> DBI_0.2-4           AnnotationDbi_1.6.1 Biobase_2.4.1
> kernlab_0.9-8
>
> loaded via a namespace (and not attached):
> [1] SSOAP_0.4-6 tools_2.9.2 XML_2.5-1
>
> Thanks,
> Kishor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>   


-- 
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M2-B876
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2 at fhcrc.org