Question: BioNet - interpretation of node score
gravatar for Eva Benito Garagorri
9.0 years ago by
Eva Benito Garagorri70 wrote:
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 (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]]
ADD COMMENTlink written 9.0 years ago by Eva Benito Garagorri70
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 282 users visited in the last hour