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In such cases, heuristics, based on different permutations and combination of available signs, symptoms and other data, guide the clinician to arrive at a hypothesis, get views from peers, try to refute the ones not aligning, order a diagnostic test and get the hypothesis confirmed.
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When the reference and test datasets are based on different microarray platforms (cDNA vs Affymetrix), the p-values were instead computed using random permutations of probes on the reference arrays.
For continuous variables, a permutation test based on difference in medians between groups is used.
The LOD threshold was obtained based on permutation test (1000 permutations, P = 0.05) for each data set.
To approximate the statistic distribution, two different resampling plans are considered; the usual one based on permutations and a new bootstrap procedure which does not require the exchangeability assumption.
To obtain a SNP-wise type I error of 0.001, we used a penalty (lambda) of 110, estimated based on 100 permutations under the null for different values of lambdas.
Significances are based on 10100 permutations evaluating whether fixation indices were different from a null distribution of variance parameters assuming samples were drawn from randomly chosen species.
The presented permutation tests are based on 1000 permutations of the fitted curves in two different categories.
SDs divergence measures in different categories were compared by means of pairwise permutation tests (based on 1000 permutations).
In order to account for the fact that some subjects were used in different pairs, we used random permutation tests, and calculated p-value based on 10,000 permutations.
"We give users insights based on those permutations about how you can work better in an environment that is very different from yours or even in one that is very similar," says Birwadker.
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