Hi, I get the "Error in pathIDsLev1" error when using the gene2pathway retrain() function. > retrain(minnmap=30, level1Only="Metabolism", level2Only="Genetic Information Processing", organism="hsa", gene2Domains=NULL, KEGG.package=TRUE, remove.duplicates=FALSE, use.bagging=TRUE, nbag=11) Retrieving KEGG information via KEGG.db package ... Error in pathIDsLev1[sapply(level1Only, function(l) grep(l, names(pathIDsLev1)))] : invalid subscript type 'list' > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] org.Hs.eg.db_2.3.6 RCurl_1.3-0 bitops_1.0-4.1 gene2pathway_1.4.0 org.Dm.eg.db_2.3.5 RBGL_1.22.0 graph_1.24.1 [8] KEGGSOAP_1.20.0 biomaRt_2.2.0 KEGG.db_2.3.5 RSQLite_0.7-3 DBI_0.2-4 AnnotationDbi_1.8.1 Biobase_2.6.0 [15] kernlab_0.9-9 loaded via a namespace (and not attached): [1] SSOAP_0.5-4 tools_2.10.0 XML_2.6-0 XMLSchema_0.1-4 Would anyone have a suggestion as what to do next? Thanks very much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer