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The significance of the pair-wise FST values were estimated by permutation analyses using 10,000 permutations with an assumption of no difference between the populations.
Pairwise comparisons FST and ΦST values were estimated by permutation analyses using 1,000 permutations with an assumption of no difference between populations.
The significance level of each trait in the two RIL mapping populations was obtained by permutation analyses using Map Manager QTX software [ 65].
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None of 10,000 permutation trials displayed results from permuted datasets that matched or exceeded the 11,037 SNPs actually observed (p<0.0001 by permutation analyses).
The commonness of gene expression in these 20 cancer types was statistically assessed by permutation analyses (p<10−5).
The same pattern is produced by pair-wise analyses using permutations of Mahalanobis distances (Additional file 3: Table S2).
A false disco-very rate was calculated for each threshold cutoff value for both pairwise analyses using permutation analysis as described by Borevitz et al.[ 1].
The present work by Carter et al. places weight on Rodin and Ohno's own statistical analyses using permutation tests: 'jumbling' as according to R. Doolittle.
Pair-wise analyses using permutations of Mahalanobis distances produce the same pattern (Additional file 3: Table S1).
These seven SNPs are based on the preliminary analyses using a permutation test with P<0.01 to indicate significance.
Statistically significant group differences in graph metrics were analysed using permutation testing (10 000 permutations) with two-tailed t-tests to investigate both increases and decreases in structural connectivity.
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