Figure 3

Evaluation of dimension reduction methods and similarity measures. Comparison of four dimension reduction methods and six similarity measures using leave-one-out cross-validation in our disease compendium. Bars and AUC estimates indicate standard errors for curves averaged over all cross-validation trials. The three similarity measures based on Pearson correlation outperform the rank-based approaches, with the p-weighted Pearson correlation proving the best at identifying other experiments of the same disease. The ICA projection method for dimension reduction outperforms the module-based approaches, and performs comparably to gene-level analysis. HsGxModules = Human Gene Expression Modules (see Methods).