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We assessed whether the derived indices were significantly different from zero using a permutation procedure (5,000 iterations) in the software ARLEQUIN version 3.1 [22].
We estimated a genomewide significance threshold using a permutation procedure.
The overall significance is then evaluated using a permutation procedure.
Linear regression and pairwise Euclidian spatial distances between individuals were tested using a permutation procedure.
The significance levels for the linkage analysis were obtained using a permutation procedure as explained in [ 19].
The significance of t-sum values themselves was evaluated using a permutation procedure described in the next section.
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To get robust p-values for the gene-environment and gene-gene interactions, we used a permutation procedure where the phenotype labels where randomly permuted between individuals.
Third, to control for the multiple comparisons that are required in the analysis of continuous data, we used a permutation procedure described by Blair and Karniski [47] to produce a reference distribution of maximum t-values (N = 216).
To identify common biomarkers in different types of cancer, we used a permutation procedure to examine if DEGs (p<0.01) are statistically consistently up-regulated or down-regulated in different types of cancer.
We used a permutation procedure to obtain a distribution of surrogate t-sum statistics.
In the case of QFAM, the module used a permutation procedure to correct for family structure.
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