Robust volcano plot: identification of differential metabolites in the presence of outliers

• Published in: BMC bioinformatics Vol. 19; no. 1; pp. 128 - 11
• Main Authors: Kumar, Nishith, Hoque, Md. Aminul, Sugimoto, Masahiro
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 11.04.2018; BioMed Central; BMC
• Subjects: Algorithms; Biomarkers - metabolism; Cardiovascular diseases; Care and treatment; Classical volcano plot; Computational biology; Diabetes; Differential metabolites; Down-Regulation - genetics; Female; Fold change; Genetic aspects; Humans; Metabolites; Metabolome; Metabolomics; Metabolomics - methods; Methodology; Receiver operating characteristic (ROC) curve; ROC Curve; Up-Regulation - genetics; Metabolomics; Differential metabolites; Fold change; Classical volcano plot; Receiver operating characteristic (ROC) curve
• DOI: 10.1186/s12859-018-2117-2
• ISSN: 1471-2105

The identification of differential metabolites in metabolomics is still a big challenge and plays a prominent role in metabolomics data analyses. Metabolomics datasets often contain outliers because of analytical, experimental, and biological ambiguity, but the currently available differential metabolite identification techniques are sensitive to outliers. We propose a kernel weight based outlier-robust volcano plot for identifying differential metabolites from noisy metabolomics datasets. Two numerical experiments are used to evaluate the performance of the proposed technique against nine existing techniques, including the t-test and the Kruskal-Wallis test. Artificially generated data with outliers reveal that the proposed method results in a lower misclassification error rate and a greater area under the receiver operating characteristic curve compared with existing methods. An experimentally measured breast cancer dataset to which outliers were artificially added reveals that our proposed method produces only two non-overlapping differential metabolites whereas the other nine methods produced between seven and 57 non-overlapping differential metabolites. Our data analyses show that the performance of the proposed differential metabolite identification technique is better than that of existing methods. Thus, the proposed method can contribute to analysis of metabolomics data with outliers. The R package and user manual of the proposed method are available at https://github.com/nishithkumarpaul/Rvolcano .