Figure 4 .

Comparison of CoGAPS and linear models. (a) Clustering diagram to compare the gene signatures in the columns of A from eq. 1 in each of three CoGAPS simulations (simulation 1 in red, simulation 2 in green, and simulation 3 in blue) to the signatures inferred from a limma linear model using the same design matrix (black). (b) and (c) display gene set statistics for pathway activity resulting from the limma estimated linear model for STAT, RAS, AKT, TGFB, and Notch (left to right within each group) colored according to the bottom figure legend. (b) Uses the standard gene set test from limma, rescaled according to eq. 4. (c) Uses the permutation-based gene set statistic adapted for a linear model from eqs. 2 and 3 described in the methods section.