MAVTgsa: An R Package for Gene Set (Enrichment) Analysis

Table 2

Results of the MANOVA, 10-fold CV error, and post hoc test (Dunnett’s method) of breast cancer data with three groups for nine pathways.

GS name	GS size	MANOVA; 𝑃-value	10-fold CV	adjusted 𝑃 value		Multiple comparisons
			Error rate	FDR	FWE	𝑇2 − 𝑇1	𝑇3 − 𝑇1
androgen_receptor_signaling	72	0.0000*	0.3438	0	0	0.2088	0.0027
apoptosis	187	0.0031*	0.3542	0.0047	0.1751	0.5836	0.0517
cell_cycle_control	31	0.0000*	0.3333	0	0	0.3823	0.0002
notch_delta_signalling	34	0.0040*	0.3750	0.0051	0.2179	0.4558	0.0468
P53_signalling	33	0.0001*	0.2917	0.0002	0.0078	0.4891	0.0029
ras_signalling	266	0.0049*	0.3542	0.0055	0.5569	0.9132	0.0239
tgf_beta_signaling	82	0.0564	0.3438	0.0564	0.4885	0.6840	0.0664
tight_junction_signaling	326	0.0001*	0.3854	0.0002	0.0294	0.2937	0.0058
wnt_signaling	176	0.0004*	0.3542	0.0007	0.3299	0.6117	0.0037

∗Denote 𝑃 values < 0.01 in Wilks’ Λ test.