Parallel analysis found this value to be greater than the expected λ95 value obtained by random permutations of residual values (λ95 = 1.7).
The Euclidean distance between the two vectors is also significantly lower than the one obtained by random permutation of the two vectors; specifically, when we performed 1,000 permutations of these values, all of them had higher Euclidean distance (P-value <0.001).
Statistical significance was evaluated using 10,000 permutations of expression values relative to the genotypes as previously described by Stranger et al [22] with a corrected p value threshold of 0.05.
Significance thresholds for interval mapping were obtained through 10,000 permutations of trait values among backcross progeny.
To test for the presence of phylogeographic structure among populations (i.e. RST significantly larger than GST), 10,000 permutations of RST values were performed.
Figures 4, 5, 6 and 7 shows the null distributions (based on 1000 permutations) of PRESS values when SNPs were selected using extreme sires or all sires in each stratum.
The p-value gives the probability of finding a higher indicator value in random permutations, with values of less than 0.1 indicating that the stage group is a significant factor.
In order to remove clearly insensitive parameters, we set to zero all s i, j that did not exceed the maximum value observed under 10000 permutations of the parameter values.
These threshold values are distributed over the whole range of each parameter and every permutation of threshold values was tested to see which one would end up with the hypnogram that has the most accordance with the pre-scored one.
For each tree, the classification accuracy of the OOB samples is determined both with and without random permutation of the values of the variable.
At the previously defined thresholds for model inclusion and exit, no family-nested QTL were found to exceed RMIPs of 0.10 upon null permutation of trait values under the employed bootstrap sampling scheme.
