Dick Beyer <dbeyer <at=""> u.washington.edu> writes: > > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Hello Dick, I have the same error. I check the code and in the function "gene2pathway:::getKEGGHierarchy" there are : kegg = RCurl:::getURL("ftp://ftp.genome.jp/pub/kegg/brite/ko/ko00001.keg") kegg = unlist(strsplit(kegg, "\n")) level1 = grep("A", kegg) level2 = grep("B ", kegg) level3 = grep("PATH", kegg) ... But if you look at the URL, in the file we found : "A01100 Metabolism" "B" "B 01101 Carbohydrate Metabolism" ... I don't know if this error has been corrected or if it will be in a futur version (with Bioc 2.6) Jean-Pierre