Table 1.

Calculation of FDRs for the sample pair S_P/R_P

		Statistical test option
Proteins	Source of significant proteins	t-test	ranksum	either	both	neither
UL	RA1	32	42	44	30	92
	RA2	31	38	41	28	99
	RA3	29	38	41	26	107
	RA4	28	40	41	27	108
	MPSP	22	29	29	22	61
IS	RA1	9	14	15	8	72
	RA2	4	10	10	4	57
	RA3	5	14	14	5	84
	RA4	5	14	14	5	68
	MPSP	1	5	5	1	28
FDR		0.045	0.172	0.172	0.045	0.459

FDRs were calculated for the sample pair S_P/R_P based on a separate quantitation of the UL protein relative abundance and the IS protein relative abundance. The fold-change was fixed at 2 and the MPSP at 4. The t-test and the Wilcoxon ranksum test were performed at a 5% significance level. RA₁, RA₂, RA₃, and RA₄ represent the protein relative abundance for the four permuted sample-pairings. Shown in a row of 'RA_x' (x = 1, 2, 3, or 4 permuted sample-pairings) are the numbers of proteins found significant by the five statistical test options, including: the t-test alone ('t-test'), the ranksum test alone ('ranksum'), either the t-test or the ranksum test ('either'), both the t-test and the ranksum test ('both'), and without a statistical test ('neither'). Shown in the two 'MPSP' rows are the UL and IS proteins, respectively, found significant in all four permuted sample-pairings. A FDR is the ratio of the number of significant IS proteins over the number of significant UL proteins.