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We intend to implement alternative methods of choosing the best value of k, such as employing the GAP statistic [37], a measure that evaluates the difference (gap) between the within-cluster sum of squares of a given partition with its expectation under a null reference distribution.
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The gap statistic was also computed using the cluster package in R, which compares within-cluster dispersion with expected dispersion under a reference null distribution simulated with 100 bootstrap replicates.
The null distribution can be generated by simulating under a null model of no positive selection.
Recall that the reconstruction table has been generated under a null hypothesis of no association.
Under a null hypothesis SNP G i has no effect on disease, rr1 = rr2 = 1.
Using this methodology, we choose to evaluate 22 models that made mechanistic sense including a null model for a reference.
Hypotheses are evaluated with reference to a null hypothesis which states that random processes create the observed data.
Moreover, the analysis is performed under the assumption of a null discount rate.
The significance of overlap is defined as P (Y > y obs ) under a bootstrapped null distribution.
a Area under the curve (AUC) for a null hypothesis was 0.5.
b For calculated score: Area under the curve (AUC) for a null hypothesis was 0.5.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com