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研究寄生虫对建立基线以避免二次分析错误的看法。

A research parasite's perspective on establishing a baseline to avoid errors in secondary analyses.

机构信息

Broad Institute of MIT and Harvard, 75 Ames St, Cambridge, MA 02142, USA.

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.

出版信息

Gigascience. 2021 Mar 12;10(3). doi: 10.1093/gigascience/giab015.

DOI:10.1093/gigascience/giab015
PMID:33710326
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC7953484/
Abstract

To enhance reproducibility in scientific research, more and more datasets are becoming publicly available so that researchers can perform secondary analyses to investigate questions the original scientists had not posited. This increases the return on investment for the NIH and other funding bodies. These datasets, however, are not perfect, and a better understanding of the assumptions that shaped them is required. The 2020 Junior Research Parasite Award recognized our work that showed that the signal-to-noise ratio in a particular dataset had not been investigated, leading to an erroneous conclusion in the original research. In this commentary, I share the process that led to the identification of the problem and hopefully provide useful lessons for other research parasites.

摘要

为了提高科学研究的可重复性,越来越多的数据集变得公开可用,以便研究人员可以进行二次分析,以研究原始科学家没有提出的问题。这增加了 NIH 和其他资助机构的投资回报。然而,这些数据集并不完美,需要更好地了解塑造它们的假设。2020 年青年研究寄生虫奖认可了我们的工作,该工作表明,特定数据集中的信噪比尚未得到研究,导致原始研究得出错误的结论。在这篇评论中,我分享了导致问题识别的过程,并希望为其他研究寄生虫提供有用的经验教训。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82d0/7953484/f4bd22346588/giab015fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82d0/7953484/f4bd22346588/giab015fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82d0/7953484/f4bd22346588/giab015fig1.jpg

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本文引用的文献

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Highlight negative results to improve science.突出负面结果以改进科学。
Nature. 2019 Oct 4. doi: 10.1038/d41586-019-02960-3.
2
Data detectives, self-love, and humility: a research parasite's perspective.数据侦探、自爱和谦逊:一个研究寄生虫的视角。
Gigascience. 2020 Jan 1;9(1). doi: 10.1093/gigascience/giz148.
3
Apparent bias toward long gene misregulation in MeCP2 syndromes disappears after controlling for baseline variations.在控制基线差异后,MECP2 综合征中长基因失调的明显偏向消失了。
Nat Commun. 2018 Aug 13;9(1):3225. doi: 10.1038/s41467-018-05627-1.
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Celebrating parasites.赞美寄生虫。
Nat Genet. 2017 Mar 30;49(4):483-484. doi: 10.1038/ng.3830.
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1,500 scientists lift the lid on reproducibility.1500名科学家揭开了可重复性的盖子。
Nature. 2016 May 26;533(7604):452-4. doi: 10.1038/533452a.
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Gene length matters in neurons.基因长度在神经元中很重要。
Neuron. 2015 Apr 22;86(2):353-5. doi: 10.1016/j.neuron.2015.03.059.
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Disruption of DNA-methylation-dependent long gene repression in Rett syndrome.雷特综合征中DNA甲基化依赖性长基因抑制的破坏。
Nature. 2015 Jun 4;522(7554):89-93. doi: 10.1038/nature14319. Epub 2015 Mar 11.
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Opinion: Reproducible research can still be wrong: adopting a prevention approach.观点:可重复的研究仍可能出错:采取预防措施。
Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):1645-6. doi: 10.1073/pnas.1421412111.
9
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.测序质量控制联盟对RNA测序准确性、可重复性和信息含量的全面评估。
Nat Biotechnol. 2014 Sep;32(9):903-14. doi: 10.1038/nbt.2957. Epub 2014 Aug 24.
10
Power failure: why small sample size undermines the reliability of neuroscience.停电:为什么小样本量会破坏神经科学的可靠性。
Nat Rev Neurosci. 2013 May;14(5):365-76. doi: 10.1038/nrn3475. Epub 2013 Apr 10.