Several options have been implemented for summarizing the gene expression profiles of a given module. For example, the function moduleEigengenes represents the module expressions of the q-th module by the module eigengene E(q), defined as the first principal component of the expression matrix. The eigengene E can be thought of as a weighted average expression profile. Eigengene calculation incorporates imputation of missing values implemented in the package impute [31,32]. Alternatively, the user can use the intramodular connectivity measure to define the most highly connected intramodular hub gene as the module representative. One can show that intramodular hub genes are highly correlated with the module eigengene [11].
