NetworkConceptsandtheirgeometricInterpretation(完美版).doc

Network Concepts and their geometric Interpretation mini R Tutorial Computation of fundamental and eigengene-based network concepts Jun Dong, Steve Horvath Correspondence: shorvath@, /biostat/people/horvath.htm This is a self-contained R software tutorial that illustrates how to compute network concepts and their eigengene based analogues. This tutorial shows how we arrived at Figure 1 and Table 3 in Horvath and Dong (2008). The microarray data set corresponds to gene expression measurements in the mouse liver tissues of female mice of an F2 mouse cross. Some familiarity with the R software is desirable but the document is fairly self-contained. To cite the methods and results of this article, please use the following references Horvath S, Dong J (2008) Geometric Interpretation of Gene Coexpression Network Analysis. PLoS Comput Biol 4(8): e1000117 Dong J, Horvath S (2007) Understanding Network Concepts in Modules, BMC Systems Biology 2007, 1:24 The WGCNA R package is described in: Langfelder P, Horvath S (2008) WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics, 2008 9:559 The tutorial, R functions, data etc can be found at the following webpage /labs/horvath/ModuleConformity/GeometricInterpretation/ Please also download the WGCNA R library from /labs/horvath/CoexpressionNetwork/Softwares/WGCNA/ To install it in R use the command Install package(s) from local zip file which can be found in the tab Packages? The WGCNA package contains our most recent R software code and accompanying software tutorials. Disclaimer: Absolutely no warranty on the code. Please contact Steve Horvath (shorvath@), Peter Langfelder (peter.langfelder@) or Jun Dong with suggestions. ####### Start of R codes ####### rm(list=ls()) setwd(C:/Documents and Settings/Steve Horvath/My Documents/ADAG/JunDong/WebpageAugust2009) # installation instructions for the following library are given above library(WGCNA) # install the following R packages from the cran webpage u