2009
DOI: 10.1089/cmb.2008.0144
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Properties of Balanced Permutations

Abstract: This paper takes a close look at balanced permutations, a recently developed sample reuse method with applications in bioinformatics. It turns out that balanced permutation reference distributions do not have the correct null behavior, which can be traced to their lack of a group structure. We find that they can give p-values that are too permissive to varying degrees. In particular the observed test statistic can be larger than that of all B balanced permutations of a data set with a probability much higher t… Show more

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Cited by 23 publications
(29 citation statements)
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“…The role of the group structure has recently been emphasized (Southworth et al. 2009 ; Goeman and Solari 2010 ). Southworth et al.…”
Section: Introductionmentioning
confidence: 99%
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“…The role of the group structure has recently been emphasized (Southworth et al. 2009 ; Goeman and Solari 2010 ). Southworth et al.…”
Section: Introductionmentioning
confidence: 99%
“…Southworth et al. ( 2009 ) note that in particular the set of ‘balanced permutations’ cannot be used, since it is not a group.…”
Section: Introductionmentioning
confidence: 99%
“…It is worth noting that the group structure of true𝕆˜ is essential for the validity of the result, as remarked in Southworth, Kim and Owen (). Furthermore, the proof extends that given in Lehmann and Romano (), which is based on a group with finite elements (such as the permutation group), to a group with uncountably infinite elements (such as the orthogonal group).…”
Section: Rotation‐based K‐fwer Controlmentioning
confidence: 62%
“…In contrast to identification (see footnote 15) randomness of the chosen permutations is important here: non-random permutation sets do not generally guarantee valid inference (e.g. Southworth et al 2009).…”
Section: A2 Consistency Of Recentered Ivsmentioning
confidence: 99%