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Finally, the distribution of the difference in means, significance of the effects and correlation coefficients was inspected for both amplitude and phase effect, and the results of the permutations were then compared to the original data.
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Column permutations are then applied to the matrix in Figure 1b, generating the configuration presented in Figure 1c, which uncovers a visual data pattern whose identification was previously much harder to perceive.
A permutation-based F-test (Fs, with 1000 permutations) was then performed and restricted maximum likelihood was used to solve the mixed model equations.
The average decrease in accuracy of these permutations is then averaged over all the trees and is used to measure the importance of the variable j.
A Mantel test with 1000 permutations was then conducted between the genetic and geographic distance matrices for each of the four allele groups using Arlequin.
Significance testing using permutations was then carried out to determine the overlap between six random samples of 20,000 values (the number of correlations) from a total of 1,236,087 values (the total number of probes).
The operation for random permutation was then applied to the aligned PWMs to generate 100 control motifs.
A sample permutation is then used to obtain P values for each gene set.
A Wilcoxon test with permutation is then used to evaluate the significance of association by comparing ranks in cases and controls.
The permutation trials were then conducted 100 times.
For each permutation, subjects were then randomly assigned to any of the groups and the F-statistic was computed again (Fpermuted).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com