[Bioc-devel] <no subject>

[Julie Zhu]

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