Dear List & Calin, I am trying to use Pathway Express from RontoTools for microarray analysis. I get the following error with keggPathwayGraphs command when I use the option "updateCache = TRUE". I want to use this option in order to download the latest KEGG pathways. Thanks & Regards, Shruti Marwaha Graduate Student Systems Biology and Physiology University of Cincinnati -- output of sessionInfo(): > library("KEGGREST") > library("ROntoTools") > kpg <- keggPathwayGraphs("hsa", updateCache = TRUE, verbose = F) NA element in edges. Error in validObject(.Object) : invalid class ???graphNEL??? object: FALSE > traceback() 15: stop(msg, ": ", errors, domain = NA) 14: validObject(.Object) 13: .local(.Object, ...) 12: initialize(value, ...) 11: initialize(value, ...) 10: new("graphNEL", nodes = nodes, edgeL = edgeL, edgemode = edgemode) 9: graphNEL(nodes = snodes, edgeL = newEdges, edgemode = edgemode(graph)) 8: subGraph(nodes, graph) 7: subGraph(nodes, graph) 6: subKEGGgraph(new.nodes, graph) 5: subGraphByNodeType(gR, "gene") 4: KEGGgraph::KEGGpathway2Graph(g) 3: FUN(X[[82L]], ...) 2: lapply(allPathwayInfo, function(g) { g <- KEGGgraph::KEGGpathway2Graph(g) kg <- new("graphNEL", nodes(g), edges(g), edgemode = "directed") if (length(getKEGGedgeData(g)) == 0) { if (verbose) setTxtProgressBar(pb, getTxtProgressBar(pb) + 1) return(NULL) } edgeDataDefaults(kg, "subtype") <- NA relGeneTable <- data.frame(cbind(do.call(rbind, strsplit(names(getKEGGedgeData(g)), "~")), sapply(getKEGGedgeData(g), function(e) paste(lapply(getSubtype(e), getName), collapse = ","))), stringsAsFactors = FALSE) names(relGeneTable) <- c("from", "to", "subtype") edgeData(kg, relGeneTable$from, relGeneTable$to, "subtype") <- relGeneTable$subtype if (verbose) setTxtProgressBar(pb, getTxtProgressBar(pb) + 1) return(kg) }) 1: keggPathwayGraphs("hsa", updateCache = TRUE, verbose = F) > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats graphics grDevices utils datasets methods base other attached packages: [1] ROntoTools_1.4.0 Rgraphviz_2.8.1 KEGGgraph_1.22.1 XML_3.98-1.1 boot_1.3-11 graph_1.42.0 [7] KEGGREST_1.4.1 loaded via a namespace (and not attached): [1] BiocGenerics_0.10.0 Biostrings_2.32.1 httr_0.4 IRanges_1.22.10 parallel_3.1.0 [6] png_0.1-7 RCurl_1.95-4.3 stats4_3.1.0 stringr_0.6.2 tools_3.1.0 [11] XVector_0.4.0 zlibbioc_1.10.0 -- Sent via the guest posting facility at bioconductor.org.