[Bioc-devel] biomaRt help
julie.zhu at umassmed.edu
Tue Jun 9 14:54:47 CEST 2009
Sorry, forgot to include subject line.
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!
> 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
> FYI, this error also occurs in the development version of R.
> Best regards,
> R version 2.9.0 (2009-04-17)
> attached base packages:
>  stats graphics grDevices utils datasets methods base
> other attached packages:
>  biomaRt_2.0.0
> loaded via a namespace (and not attached):
>  RCurl_0.94-1 XML_2.3-0
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