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For PMA experiments, the SCCA parameters were automatically tuned using a permutation scheme provided in PMA.
In a second analysis, we tested each AFLP marker for associations between band frequency and altitude of the sampling site using a permutation scheme which accounted for the hierarchical structure in the data.
The FDR was estimated using a permutation scheme as implemented in the pamr R-package, and the relatively low FDR (only about 17%% of the 67 CpGs are expected to be false positives) demonstrates the presence of a genuine DNAme signal associated with HOTAIR expression.
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Since the two sets are very different in size (81 for WBC versus 1463 for OO), we did not use a permutation scheme to select subsets for comparison (Kerr, 2009).
The newly identified genes were further filtered using a permutation test.
Empirical values for chromosome-wise significance thresholds were determined using a permutation test.
P values were computed using a permutation test (10,000 permutations).
The difference between the two sets of residuals was tested using a permutation approach (10,000 permutations).
The pfp is calculated using a permutation based procedure (100,000 permutations were conducted).
The significance of differentiation was examined using a permutation test with 1000 permutations.
We estimated a genomewide significance threshold using a permutation procedure.
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