论文题目：Transformation, Normalization, and Batch Effect in the Analysis of Mass Spectrometry Data for Omics Studies
scholar 引用：8
页数：294 来自book：Statistical Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry
发表时间：2012
作者：Bart J.A. Mertens
正文组织架构：
3. Batch Effect in Omics Studies
3.1 Time-Fixed Batch Effects
3.2 Time-Dependent Batch Effects
正文部分内容摘录：
- we can sometimes manipulate or modify the experiment to account for the known structure so that it is rendered innocuous and cannot unduly affect conclusions. 设计好实验
- Even better, we may be able to remove (part of) the effects due to batch structure, by taking suitable precautions at the experimental design stage. 通过实验设计阶段采取的预防措施，可以消除部分批次效应。但这是后续的数据分析人员无法控制的吧？
- In contrast to genetics, batch effect is much more problematic within proteomics and metabolomics, which is due to the measurement procedures involved.蛋白质组学和代谢组学中，批次效应影响更大。
- 蛋白质组学研究中批次效应的两个步骤：
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To control the experimental design as much as possible in advance of the experiment to maximize our options to either remove or account for batch effect at the analysis stage.
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To exploit the chosen structure afterwards to either remove or adjust for the batch variation in the analysis.
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The objectives of these steps are at least threefold.
1. To ensure experimental validity (the experiment can deliver the required results)
2. To improve robustness of the experiment (conclusions will still be valid, even when experimental execution differs from experimental planning)
3. To improve (statistical) efficiency of effect estimates based on the data (statistical summaries will have lower variation).
3.1 Time-Fixed Batch Effects 好像都是跟实验条件有关
- plates in mass spectrometry
- freezer used for sample storage
- change of cleaning or work-up fluid for sample processing
- batches of beads or cartridges for protein fractionation
- instrument re-calibration.
- The excellent performance of the blocked version of the experiment again emphasizes the need and importance of pro-actively designing and implementing block-randomized experiments when batch structures are identified in advance of the experimentation. 实验设计非常重要
3.2 Time-Dependent Batch Effects
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longitudinal experimentation, long observation tracks with repeated measurement per individual 每个人重复测量
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sample collection across extended time periods, patient accrual spread across an extended period of time 长时间采样，患者贯穿时间段
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time-indexed samples or instrument calibrations 样本的时间索引或者仪器校正
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distinct days of measurement or sample processing.
