Hi Colin, There appears to be a problem with the construction of the sql query for aafGO when using the yeast2.db package: > suppressMessages(library(annaffy)) > suppressMessages(library(yeast2.db)) > ids <- head(Lkeys(yeast2CHR)) > aafGO(ids, "yeast2.db") Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: cannot join using column gene_id - column not present in both tables) Best, Jim -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues