一种新的生物信息学方法,用于鉴定当前代谢组学研究中表现始终良好的标准化策略。

A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies.

机构信息

Ph.D. candidates of Zhejiang University, China, and jointly cultivated by the School of Pharmaceutical Sciences in Chongqing University, China. Their main research interests include OMICs-based bioinformatics and statistical metabolomics.

出版信息

Brief Bioinform. 2020 Dec 1;21(6):2142-2152. doi: 10.1093/bib/bbz137.

Abstract

Unwanted experimental/biological variation and technical error are frequently encountered in current metabolomics, which requires the employment of normalization methods for removing undesired data fluctuations. To ensure the 'thorough' removal of unwanted variations, the collective consideration of multiple criteria ('intragroup variation', 'marker stability' and 'classification capability') was essential. However, due to the limited number of available normalization methods, it is extremely challenging to discover the appropriate one that can meet all these criteria. Herein, a novel approach was proposed to discover the normalization strategies that are consistently well performing (CWP) under all criteria. Based on various benchmarks, all normalization methods popular in current metabolomics were 'first' discovered to be non-CWP. 'Then', 21 new strategies that combined the 'sample'-based method with the 'metabolite'-based one were found to be CWP. 'Finally', a variety of currently available methods (such as cubic splines, range scaling, level scaling, EigenMS, cyclic loess and mean) were identified to be CWP when combining with other normalization. In conclusion, this study not only discovered several strategies that performed consistently well under all criteria, but also proposed a novel approach that could ensure the identification of CWP strategies for future biological problems.

摘要

在当前的代谢组学中,经常会遇到不需要的实验/生物变异和技术误差,这就需要采用归一化方法来消除不需要的数据波动。为了确保“彻底”去除不需要的变化,需要综合考虑多个标准(“组内变异”、“标志物稳定性”和“分类能力”)。然而,由于可用的归一化方法数量有限,因此很难找到能够满足所有这些标准的合适方法。在此,提出了一种新的方法来发现所有标准下表现一致良好(CWP)的归一化策略。基于各种基准,发现当前代谢组学中流行的所有归一化方法都不是 CWP。“然后”,发现了 21 种新的策略,这些策略将基于“样本”的方法与基于“代谢物”的方法相结合,是 CWP。“最后”,当与其他归一化方法结合时,确定了各种当前可用的方法(如三次样条、范围缩放、水平缩放、EigenMS、循环局部均值和均值)是 CWP。总之,本研究不仅发现了在所有标准下表现一致良好的几种策略,还提出了一种新的方法,可以确保为未来的生物学问题确定 CWP 策略。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/963c/7711263/1805c8ce6595/bbz137f1.jpg

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