Hi, 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, J?r?mie > > > library(biomaRt) > human = useMart("ensembl", dataset = "hsapiens_gene_ensembl") Checking attributes and filters ... ok > path <- getBM(attributes = c("external_gene_id","go_biological_proce ss_id","go_biological_process_linkage_type"), filters = "biol_process", values = "GO:0006996", mart = human) V1 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) i386-pc-mingw32 locale: LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY= French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 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 > J?r?mie 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 http://www.msbi.nl/lebrec