Repeatability of published microarray gene expression analyses
Repeatability of published microarray gene expression analyses
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DOI：
10.1038/ng.295
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发表时间：
2009-02-01
期刊：
影响因子：
30.8
通讯作者：
van Noort, Vera
中科院分区：
文献类型：
--
作者：
Ioannidis, John P. A.;Allison, David B.;van Noort, Vera
鉴于基于微阵列的基因表达研究的复杂性，指南鼓励透明的设计和公开的数据可用。一些期刊需要公共数据存储，并且有几个公共数据库。然而，并不是所有的数据都是公开的，即使可以获得，发表的结果是否可以被独立科学家复制也是未知的。在这里，我们评估了2005-2006年发表在《自然遗传学》上的18篇关于基于微阵列的基因表达谱的文章中数据分析的重复性。每篇文章中的一个表格或数字由两个分析师团队独立评估。我们原则上复制了两个分析，部分地或有一些差异地复制了六个；无法复制十个。复制失败的主要原因是数据不可用，差异主要是由于数据注释不完整或数据处理和分析规范。发表的微阵列研究的重复性显然是有限的。应考虑制定更严格的发布规则，以确保公开数据的可用性，并明确描述数据处理和分析。
Given the complexity of microarray-based gene expression studies, guidelines encourage transparent design and public data availability. Several journals require public data deposition and several public databases exist. However, not all data are publicly available, and even when available, it is unknown whether the published results are reproducible by independent scientists. Here we evaluated the replication of data analyses in 18 articles on microarray-based gene expression profiling published in Nature Genetics in 2005-2006. One table or figure from each article was independently evaluated by two teams of analysts. We reproduced two analyses in principle and six partially or with some discrepancies; ten could not be reproduced. The main reason for failure to reproduce was data unavailability, and discrepancies were mostly due to incomplete data annotation or specification of data processing and analysis. Repeatability of published microarray studies is apparently limited. More strict publication rules enforcing public data availability and explicit description of data processing and analysis should be considered.