[Bioc-devel] biomaRt help

[Julie Zhu]

Sorry, forgot to include subject line.

Best regards,

Julie


On 6/8/09 10:17 AM, "Julie Zhu" <julie.zhu at umassmed.edu> wrote:

> Dear BiomaRt developers,
> 
> The following code using biomaRt sometimes produces error but sometimes not.
> Could you please help me to resolve the issue? Thanks a lot for your help!
> 
> Library(biomaRt)
> mart <- useMart(biomart="ensembl", dataset="drerio_gene_ensembl")
> seq1 = getSequence(id = "ENSDARG00000054562",
>             type = "ensembl_gene_id", seqType = "gene_exon_intron",
>              upstream = 350, mart = mart)
> Error in getBM(c(seqType, type), filters = c(type, "upstream_flank"),  :
>>   Query ERROR: caught BioMart::Exception::Usage: Filter upstream_flank NOT
>> FOUND
> 
> FYI, this error also occurs in the development version of R.
>  
> Best regards,
> 
> Julie
> 
>  sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
> 
> locale:
> en_US.UTF-8/en_US.UTF-8/C/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_2.0.0
> 
> loaded via a namespace (and not attached):
> [1] RCurl_0.94-1 XML_2.3-0
>