Kulinskaya E, Lewin A
Statistical Advisory Service, Imperial College, South Kensington Campus, 8 Princes Gardens, London, UK.
Ann Hum Genet. 2009 Mar;73(2):253-62. doi: 10.1111/j.1469-1809.2008.00501.x. Epub 2009 Jan 23.
This paper concerns several important points when testing for Hardy-Weinberg equilibrium (HWE) and linkage disequilibrium (LD) in genetics. First, we challenge the necessity of using exclusively two-sided tests for LD. Next, we show that the exact 2-sided tests based on the most popular measures of LD are not equivalent, and neither are the standard statistical tests even though the 1-sided tests are equivalent. We show how this results in different inference about LD for two data sets consisting of small groups of markers. Finally, we advocate the use of the conditional p-value for both LD and HWE testing. An important advantage of this p-value is that equivalent 1-sided tests are transformed into equivalent 2-sided tests.
本文涉及遗传学中哈迪-温伯格平衡（HWE）和连锁不平衡（LD）检验时的几个要点。首先，我们质疑对LD仅使用双侧检验的必要性。其次，我们表明基于最常用的LD度量的精确双侧检验并不等价，标准统计检验也不等价，尽管单侧检验是等价的。我们展示了这如何导致对由少量标记组成的两个数据集的LD得出不同的推断。最后，我们提倡在LD和HWE检验中使用条件p值。这个p值的一个重要优点是等价的单侧检验被转换为等价的双侧检验。
