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-值直方图:推断与诊断

-Value Histograms: Inference and Diagnostics.

作者信息

Breheny Patrick, Stromberg Arnold, Lambert Joshua

机构信息

Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA.

Department of Statistics, University of Kentucky, Lexington, KY 40508, USA.

出版信息

High Throughput. 2018 Aug 31;7(3):23. doi: 10.3390/ht7030023.

Abstract

It is increasingly common for experiments in biology and medicine to involve large numbers of hypothesis tests. A natural graphical method for visualizing these tests is to construct a histogram from the -values of these tests. In this article, we examine the shapes, both regular and irregular, that these histograms can take on, as well as present simple inferential procedures that help to interpret the shapes in terms of diagnosing potential problems with the experiment. We examine potential causes of these problems in detail, and discuss potential remedies. Throughout, examples of irregular-looking -value histograms are provided and based on case studies involving real biological experiments.

摘要

在生物学和医学实验中,涉及大量假设检验的情况越来越普遍。一种直观呈现这些检验的自然图形方法是根据这些检验的P值构建直方图。在本文中,我们研究了这些直方图可能呈现的规则和不规则形状,并介绍了简单的推断程序,这些程序有助于从诊断实验潜在问题的角度来解释这些形状。我们详细研究了这些问题的潜在原因,并讨论了可能的补救措施。全文提供了看起来不规则的P值直方图的示例,并基于涉及真实生物学实验的案例研究。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9154/6164648/64874b963ed5/high-throughput-07-00023-g001.jpg

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本文引用的文献

1
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions.
Brief Bioinform. 2018 Sep 28;19(5):776-792. doi: 10.1093/bib/bbx008.
2
Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation.
Nat Biotechnol. 2016 Dec;34(12):1287-1291. doi: 10.1038/nbt.3682. Epub 2016 Sep 26.
3
Analytic P-value calculation for the higher criticism test in finite problems.
Biometrika. 2014;101(4):964-970. doi: 10.1093/biomet/asu033.
4
Activity-dependent genes in mouse olfactory sensory neurons.
Chem Senses. 2014 Jun;39(5):439-49. doi: 10.1093/chemse/bju015. Epub 2014 Apr 1.
5
Secretory antibodies in breast milk promote long-term intestinal homeostasis by regulating the gut microbiota and host gene expression.
Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3074-9. doi: 10.1073/pnas.1315792111. Epub 2014 Feb 3.
6
Higher criticism thresholding: Optimal feature selection when useful features are rare and weak.
Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14790-5. doi: 10.1073/pnas.0807471105. Epub 2008 Sep 24.
7
The effects of normalization on the correlation structure of microarray data.
BMC Bioinformatics. 2005 May 16;6:120. doi: 10.1186/1471-2105-6-120.
8
Exploration, normalization, and summaries of high density oligonucleotide array probe level data.
Biostatistics. 2003 Apr;4(2):249-64. doi: 10.1093/biostatistics/4.2.249.

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