Table 2 

Empirical Data Study: Impact of the Number of Permutations 

# Permutations 
99/999/9,999 
99/999 
99/9,999 
999/9,999 



Tree 
W 
U 
W 
U 
W 
U 
W 
U 


p = 0.01 
16 
48 
14 
35 
13 
36 
5 
25 
p = 0.02 
7 
27 
5 
27 
6 
27 
3 
0 
p = 0.03 
4 
22 
3 
17 
4 
19 
1 
8 
p = 0.04 
2 
18 
1 
17 
2 
18 
1 
1 
p = 0.05 
1 
8 
0 
8 
1 
7 
1 
1 


The table outlines the impact of the number of permutations on the distribution of significant and insignificant links for distinct pvalues. Column (99/999/9,999) indicates the number of links that have a different significance than at least one of the other runs. 

Stamatakis et al. BMC Bioinformatics 2007 8:405 doi:10.1186/147121058405 