Hi, I used RamiGO to produce .gml file so that I can load my file to Cytoscape. However, when I followed your sample code in the user manual, goIDs <- c("GO:0051130","GO:0019912","GO:0005783") color <- c("lightblue","red","yellow") dd <- getAmigoTree(goIDs=goIDs,color=color,filename="example.gml",picT ype="dot",saveResult=FALSE) tt <- readAmigoDot(object=dd) ## exportCytoGML is called inside adjM2gml adjM2gml(adjMatrix(tt),relations(tt)$color,annot(tt)$fillcolor,annot(t t)$GO_ID,annot(tt)$description,filename="example.gml") I found there is an error in output gml file. In the gml file, I can find only 33 nodes, however, the in last 3 edges, there are source 34 (source node id 34). It seems that the node index starts from 0, however, in edge, the source and target are indexed from 1. thanks for help Tim -- output of sessionInfo(): R version 2.14.0 (2011-10-31) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] RamiGO_1.0.0 gsubfn_0.6-2 proto_0.3-9.2 xtable_1.7-0 org.Sc.sgd.db_2.6.4 genefilter_1.36.0 [7] annotate_1.32.3 GO.db_2.6.1 GOstats_2.20.0 RSQLite_0.11.1 DBI_0.2-5 graph_1.32.0 [13] Category_2.20.0 AnnotationDbi_1.16.19 Biobase_2.14.0 loaded via a namespace (and not attached): [1] GSEABase_1.16.1 igraph_0.6-2 IRanges_1.12.6 png_0.1-4 RBGL_1.30.1 RCurl_1.91-1.1 RCytoscape_1.4.4 splines_2.14.0 [9] survival_2.36-10 tcltk_2.14.0 tools_2.14.0 XML_3.9-4.1 XMLRPC_0.2-4 -- Sent via the guest posting facility at bioconductor.org.