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Chunk #22 — Permutation testing

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Detecting multiple associations in genome-wide studies.
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A further approach is to assume that the sampled markers are representative of an 'effective number' of independent tests [47-50]. After estimating this number -- for example, from the singular-valued decomposition of the genotype correlation matrix[50] -- asymptotic formulae can be applied. There is no formal basis for this approach, however, and studies based on real data indicate that the results are not always accurate;[51] indeed, there may be no such effective number after all [33]. This approach is not recommended; however, if it is used, all significant results should be confirmed by a permutation test.