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We consider two approaches to estimating this threshold, accounting for the correlation within the genome: one based on a permutation scheme, and the other using linear algebra to estimate an effective number of tests directly from genotype data [ Patterson et al., 2006].
The GA is based on a permutation chromosome, a split procedure and local search.
The RSA resulted in 12 significant clusters (family-wise error corrected (FWE) p < 0.05 based on a permutation test; Fig. 3).
For each test, the t-value was extracted, and its significance was estimated based on a permutation test (1000 permutations, SM-E 80. SM-E 80
This overlap in the structural space of protein protein interfaces is significantly small, with a p-value < 0.0001, based on a permutation test on the total set of protein protein interfaces.
LOD threshold for each dataset was set based on a permutation test (1,000 permutation, P = 0.05).
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This procedure is based on a permutation-based test of multivariate homogeneity of group dispersions (variance in the sites) [ 39].
SCAs are selected based on a permutation-generated null distribution and Bonferroni correction.
Pairs of treatment group data underwent permutation analysis for differential expression (PADE) that accounts for false positives by tabulating a false discovery rate (FDR) based on a permutation-generated reference curve (technical information on REDI and PADE analyses available at www.expressionanalysis.com).
The CCA for six environmental variables and four ELHTs yielded a significant biplot based on a global permutation test (1000 permutations; p<0.01; Fig. 1).
This level of coincidence also exceeded what would be expected just by chance (bootstrapped P-value < 0.05) based on a circular permutation test.
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