候选基因甲基化研究中的多重检验校正。
Correction for multiple testing in candidate-gene methylation studies.
机构信息
National Center for PTSD, VA Boston Healthcare System, Boston, MA 02130, USA.
Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA.
出版信息
Epigenomics. 2019 Jul;11(9):1089-1105. doi: 10.2217/epi-2018-0204. Epub 2019 Jun 26.
Abstract
We compared the performance of multiple testing corrections for candidate gene methylation studies, namely Sidak (accurate Bonferroni), false-discovery rate and three adjustments that incorporate the correlation between CpGs: extreme tail theory (ETT), Gao (GEA), and Li and Ji methods. The experiment-wide type 1 error rate was examined in simulations based on Illumina EPIC and 450K data. For high-correlation genes, Sidak and false-discovery rate corrections were conservative while the Li and Ji method was liberal. The GEA method tended to be conservative unless a threshold parameter was adjusted. The ETT yielded an appropriate type 1 error rate. For genes with substantial correlation across measured CpGs, GEA and ETT can appropriately correct for multiple testing in candidate gene methylation studies.
摘要
我们比较了候选基因甲基化研究中多重检验校正的性能，即 Sidak（准确的 Bonferroni）、错误发现率以及三种考虑 CpG 之间相关性的调整方法：极端尾部理论（ETT）、Gao（GEA）和 Li 和 Ji 方法。我们基于 Illumina EPIC 和 450K 数据进行了模拟，以检查实验范围内的第一类错误率。对于高相关基因，Sidak 和错误发现率校正方法较为保守，而 Li 和 Ji 方法则较为宽松。除非调整阈值参数，否则 GEA 方法往往较为保守。ETT 产生了适当的第一类错误率。对于在测量的 CpG 之间具有显著相关性的基因，GEA 和 ETT 可以适当校正候选基因甲基化研究中的多重检验。
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Nature. 2018 Oct;562(7726):203-209. doi: 10.1038/s41586-018-0579-z. Epub 2018 Oct 10.
2
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Nature. 2018 Oct;562(7726):210-216. doi: 10.1038/s41586-018-0571-7. Epub 2018 Oct 10.
3
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