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The experimental section was designed according to a factorial design of fixed effects and the analysis based on the Permutations Test for an Analysis of Variance Design.
The Ranking Metric based on the permutations is displayed in Fig. 4, where the first column is the victimisation rate ranking, (V^{(1)}), with the counties that suffer the higher rates in the upper part, and the second column displays the perception of security ranking, S, with the counties perceived as the least secure in the upper part.
Therefore, we calculate the false discovery rate (FDR) based on the permutations using a similar method introduced in GSEA [35].
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We computed the p-values for each weight value by 10000 permutations, by permuting the sample labels based on the permutation events.
There were a few other pairs with only one homozygous group deviating from the null distribution (p-values <0.05) based on the permutation tests, and the signal was not as strong.
This algorithm is based on the permutation representation of solutions.
(2010a), which is based on the permutation level of operations to obtain the distance between two solutions.
The LOD thresholds based on the permutation test were very high because we used the F2 generations for QTL analysis.
The variable selection criteria as well as the splitting procedure are based on the permutation test framework developed by Strasser and Weber (1999).
Based on the permutation and combination of three continuous nucleotides or bases, the degenerate triad NNK (N: A/C/G/T; K: G/T) can constitute 32 codons (containing a terminator codon of TAG), which can encode all kinds of 20 amino acids.
Based on the permutation test, the optimal threshold of the Pearson correlation coefficient (PCC) values for co-expression analysis in the japonica background (rice lines Mudanjiang 8 and Rb49) and indica background (rice lines IR24 and IRBB13) were determined as 0.66 and 0.73 with a false discovery rate of 0.001, respectively (Additional file 1: Figures S3 and S4).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com