[BioC] Error accessing archived sequences for Zv7

[Julie Zhu]

Hi Steffen,

I encountered the following error while trying to obtain the sequence using
archived sequence data from Zv7. Your help is greatly appreciated.

Best regards,

Julie


mart <- useMart(biomart="ensembl_mart_51", dataset="drerio_gene_ensembl",
archive=TRUE)
Checking attributes ... ok
Checking filters ... Ok

seq1 = getSequence(id = "ENSDARG00000054562",
             type = "ensembl_gene_id", seqType = "gene_exon_intron",
                upstream = 350, mart = mart)

Error in martCheck(mart, "ensembl") :
  This function only works when used with the ensembl BioMart

> 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] org.Hs.eg.db_2.2.11   RSQLite_0.7-1         DBI_0.2-4
 [4] biomaRt_2.0.0 

loaded via a namespace (and not attached):
[1] MASS_7.2-46     RCurl_0.94-1    splines_2.9.0   survival_2.35-4
tools_2.9.0   
[6] XML_2.5-3     


*******************************************
Julie Zhu, Ph.D
Research Assistant Professor
Program Gene Function and Expression
University of Massachusetts Medical School
364 Plantation Street, Room 613
Worcester, MA 01605
508-856-5256
http://www.umassmed.edu/pgfe/faculty/zhu.cfm