Concordance-Based Batch Effect Correction for Large-Scale Metabolomics

代谢组 化学 代谢组学 样品(材料) 比例(比率) 一致性 统计 批处理 样本量测定 生物系统 数据挖掘 色谱法 计算机科学 生物信息学 数学 物理 生物 量子力学 程序设计语言
作者
Fanjing Guo,Genjin Lin,Liheng Dong,Kian-Kai Cheng,Lingli Deng,Xiangnan Xu,Daniel Raftery,Jiyang Dong
出处
期刊:Analytical Chemistry [American Chemical Society]
卷期号:95 (18): 7220-7228 被引量:2
标识
DOI:10.1021/acs.analchem.2c05748
摘要

For a large-scale metabolomics study, sample collection, preparation, and analysis may last several days, months, or even (intermittently) over years. This may lead to apparent batch effects in the acquired metabolomics data due to variability in instrument status, environmental conditions, or experimental operators. Batch effects may confound the true biological relationships among metabolites and thus obscure real metabolic changes. At present, most of the commonly used batch effect correction (BEC) methods are based on quality control (QC) samples, which require sufficient and stable QC samples. However, the quality of the QC samples may deteriorate if the experiment lasts for a long time. Alternatively, isotope-labeled internal standards have been used, but they generally do not provide good coverage of the metabolome. On the other hand, BEC can also be conducted through a data-driven method, in which no QC sample is needed. Here, we propose a novel data-driven BEC method, namely, CordBat, to achieve concordance between each batch of samples. In the proposed CordBat method, a reference batch is first selected from all batches of data, and the remaining batches are referred to as "other batches." The reference batch serves as the baseline for the batch adjustment by providing a coordinate of correlation between metabolites. Next, a Gaussian graphical model is built on the combined dataset of reference and other batches, and finally, BEC is achieved by optimizing the correction coefficients in the other batches so that the correlation between metabolites of each batch and their combinations are in concordance with that of the reference batch. Three real-world metabolomics datasets are used to evaluate the performance of CordBat by comparing it with five commonly used BEC methods. The present experimental results showed the effectiveness of CordBat in batch effect removal and the concordance of correlation between metabolites after BEC. CordBat was found to be comparable to the QC-based methods and achieved better performance in the preservation of biological effects. The proposed CordBat method may serve as an alternative BEC method for large-scale metabolomics that lack proper QC samples.
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