[BioC] Problem using 'biol_process' filter in biomaRt

J.J.P.Lebrec at lumc.nl J.J.P.Lebrec at lumc.nl
Wed Oct 8 21:36:02 CEST 2008


I am having trouble retrieving GO annotations data using the 'biol_process' filter in biomaRt. I used the below code several months ago and it worked fine. The filter is NOT FOUND although it is definitely part of the listed filters as shown below.

Thanks in advance for your help,


> library(biomaRt)
> human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
Checking attributes and filters ... ok
> path <- getBM(attributes = c("external_gene_id","go_biological_process_id","go_biological_process_linkage_type"), filters = "biol_process", values = "GO:0006996", mart = human)
1 Query ERROR: caught BioMart::Exception::Usage: Filter biol_process NOT FOUND
Erreur dans getBM(attributes = c("external_gene_id", "go_biological_process_id",  : 
  Number of columns in the query result doesn't equal number of attributes in query.  This is probably an internal error, please report.
> listFilters(human)[19,]
           name description
19 biol_process        <NA>
> sessionInfo()
R version 2.7.0 (2008-04-22) 


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_1.14.1 RCurl_0.9-3   

loaded via a namespace (and not attached):
[1] tools_2.7.0  XML_1.94-0.1

Jérémie Lebrec
Dept. of Medical Statistics and Bioinformatics
Leiden University Medical Center
Postzone S-05-P
P.O. Box 9600
2300 RC Leiden
The Netherlands
j.j.p.lebrec at lumc.nl

More information about the Bioconductor mailing list