. 2015 Sep 28;10(9):e0138810. doi: 10.1371/journal.pone.0138810

Table 7. Performance evaluation in pairwise comparison tests using four methods (ANOVA, LIMMA, KW and Proposed) for the small-sample case.

Adjusted p-value < 0.05
Pair of groups	Predicted DR ${(log \frac{{\hat{μ}}_{i}}{{\hat{μ}}_{j}} < - 1)}^{a}$	True DR	Correctly predicted DR	Predicted UR ${(log \frac{{\hat{μ}}_{i}}{{\hat{μ}}_{j}} > + 1)}^{a}$	True UR	Correctly predicted UR
	Without outlying expressions
G1 vs. G2	{49, 51, 50, 49}	50	{49, 50, 50, 49}	{101, 100, 98, 101}	100	{100, 99, 98, 100}
G1 vs. G3	{130, 129, 130, 130}	130	{130, 129, 130, 130}	{99, 102, 101, 99}	100	{99, 100, 100, 99}
G1 vs. G4	{50, 49, 49, 50}	50	{50, 49, 48, 50}	{101, 100, 99, 101}	100	{100, 99, 99, 100}
G2 vs. G3	{100, 101, 102, 100}	100	{99, 100, 100, 99}	{20, 19, 20, 20}	20	{20, 19, 20, 20}
G2 vs. G4	{51, 49, 47, 51}	50	{50, 49, 47, 50}	{49, 50, 49, 49}	50	{49, 50, 49, 49}
G3 vs. G4	{50, 50, 51, 50}	50	{49, 48, 50, 49}	{132, 128, 129, 132}	130	{130, 128, 129, 130}
	With a single outlying expression in 10% genes
G1 vs. G2	{37, 31, 41, 49}	50	{37, 31, 41, 49}	{83, 74, 84, 100}	100	{83, 74, 84, 100}
G1 vs. G3	{107, 90, 112, 130}	130	{107, 90, 112, 130}	{83, 76, 84, 99}	100	{83, 76, 84, 99}
G1 vs. G4	{43, 38, 43, 50}	50	{43, 38, 43, 50}	{83, 69, 83, 101}	100	{83, 69, 83, 100}
G2 vs. G3	{84, 69, 87, 100}	100	{84, 69, 87, 99}	{15, 12, 16, 20}	20	{15, 12, 16, 20}
G2 vs. G4	{43, 36, 43, 51}	50	{43, 36, 43, 50}	{37, 27, 43, 49}	50	{37, 27, 43, 49}
G3 vs. G4	{43, 37, 43, 50}	50	{43, 37, 43, 49}	{107, 87, 117, 131}	130	{107, 87, 117, 130}

We generated 300 DE genes out of 20,000 total genes for m = 4 conditions with different patterns for a small-sample case (n1 = n2 = n3 = n4 = 6) and σ ² = 0.05, with a 2-fold change in expression between the groups, to investigate the pattern-detection performance of the proposed method in comparison with the others. The values reported in the form {x, x, x, x} in this table represent the numbers of downregulated (DR) or upregulated (UR) differentially expressed (DE) genes estimated by the ANOVA, LIMMA, KW and proposed (Bold) methods, respectively. ^aNote that $log \frac{{\hat{μ}}_{i}}{{\hat{μ}}_{j}} < - 1$ indicates significant 2-fold downregulation and $log \frac{{\hat{μ}}_{i}}{{\hat{μ}}_{j}} > + 1$ indicates significant 2-fold upregulation.