Dear List, I have recently started exploring the Package ‘BioNet’ for network analysis of microarray data. I have a fundamental question about the interpretation of the results. From my understanding, BioNet first takes a series of p-values, fits them to a model, and then uses this information to score the nodes of a given network (the package is based on a human protein-protein interaction network) and output the best scoring subnetwork. In the 2D visualization of this subnetwork, squares represent nodes with a negative score and circles represent nodes with a positive score. What I do not understand is what the sign of the scores represents, i.e., what is the interpretation of an interaction between two positive nodes vs the interaction of two negative nodes? I am attaching the code from the BioNet Tutorial for the introductory example, only I am not aggregating the pvalues, but rather just taking the pvalues for differential expression (because I am only using this information for my own data). I also changed the FDR threshold so that the resulting network would be smaller. Thanks a lot in advance. Best, Eva ---------- Eva Benito Garagorri PhD program in Neurosciences Institute for Neurosciences in Alicante UMH-CSIC San Juan de Alicante 03550 Spain ebenito@umh.es (34) 965 91 92 33 ---------------- library(BioNet) library(DLBCL) data(dataLym) data(interactome) pvals=dataLym$t.pval names(pvals)=dataLym$label subnet=subNetwork(dataLym$label,interactome) subnet=rmSelfLoops(subnet) fb=fitBumModel(pvals,plot=FALSE) scores=scoreNodes(subnet,fb,fdr=0.000001) module=runFastHeinz(subnet,scores) logFC=dataLym$diff names(logFC)=dataLym$label plotModule(module,scores=scores,diff.expr=logFC) ---------- > sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] es_ES.UTF-8/es_ES.UTF-8/C/C/es_ES.UTF-8/es_ES.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] DLBCL_1.2 BioNet_1.6.5 RBGL_1.24.0 graph_1.26.0 Biobase_2.8.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.10.2 DBI_0.2-5 igraph_0.5.4 [4] RSQLite_0.9-2 tools_2.11.1 XML_3.1-0 > [[alternative HTML version deleted]]