Table 2.

Comparison of the number of significant peptides by FDR in the Salmonella data (left) and simulation data (right)

	Salmonella typhi			Simulation
FDR	0.01	0.05	0.10	0.01	0.05	0.10
Raw	266	399	473	0	58	77
EigenMS	444	476	476	80	82	87
Global	211	312	372	96	150	172
Smoothing	245	345	412	200	200	200
ANOVA	462	476	476	60	79	80

In the simulation, there were 200 peptides, of which only 80 were differentially expressed.