Table 4:

The average correlation between preprocessing methods across the compendium of 30 experiments

	fRMA— default	GCRMA— default	MBEI— no MM	MBEI— default	MAS5.0— default	PLIER— no MM	PLIER— default	RMA— default	RMA— no BG
t2-statistic
fRMA—default	1.00	0.60	0.63	0.62	0.61	0.78	0.61	0.77	0.77
GCRMA—default	0.60	1.00	0.54	0.59	0.59	0.61	0.57	0.63	0.62
MBEI—no MM	0.63	0.54	1.00	0.67	0.50	0.68	0.57	0.66	0.66
MBEI—default	0.62	0.59	0.67	1.00	0.59	0.64	0.64	0.64	0.64
MAS5.0—default	0.61	0.59	0.50	0.59	1.00	0.59	0.53	0.60	0.60
PLIER—no MM	0.78	0.61	0.68	0.64	0.59	1.00	0.63	0.87	0.88
PLIER—default	0.61	0.57	0.57	0.64	0.53	0.63	1.00	0.62	0.62
RMA—default	0.77	0.63	0.66	0.64	0.60	0.87	0.62	1.00	0.93
RMA—no BG	0.77	0.62	0.66	0.64	0.60	0.88	0.62	0.93	1.00
Bayesian network
fRMA—default	1.00	0.49	0.47	0.47	0.42	0.64	0.33	0.61	0.60
GCRMA—default	0.49	1.00	0.41	0.46	0.42	0.50	0.35	0.52	0.51
MBEI—no MM	0.47	0.41	1.00	0.52	0.36	0.52	0.31	0.49	0.49
MBEI—default	0.47	0.46	0.52	1.00	0.41	0.47	0.37	0.47	0.47
MAS5.0—default	0.42	0.42	0.36	0.41	1.00	0.42	0.32	0.42	0.42
PLIER—no MM	0.64	0.50	0.52	0.47	0.42	1.00	0.34	0.74	0.77
PLIER—default	0.33	0.35	0.31	0.37	0.32	0.34	1.00	0.34	0.33
RMA—default	0.61	0.52	0.49	0.47	0.42	0.74	0.34	1.00	0.86
RMA—no BG	0.60	0.51	0.49	0.47	0.42	0.77	0.33	0.86	1.00

Spearman rank correlation coefficients are computed using P-values from either a t²-statistic or a test of the equivalence of Bayesian networks. The upper table is based on Pairwise Spearman rank correlation coefficients of P-values (GSA methods based on t-statistic and Bayesian network equivalent test) were calculated for each data set, and preprocessing pair. The maximum standard error among entries is 0.037.

Note: MM, mismatch; BG, background correction.