Resolution:
## 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.
Fertig |