Zhan X, Patterson AD, Ghosh D. Kernel approaches for differential expression analysis of mass spectrometry-based metabolomics data.
BMC Bioinformatics 2015;
16:77. [PMID:
25887233 PMCID:
PMC4359587 DOI:
10.1186/s12859-015-0506-3]
[Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 02/20/2015] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND
Data generated from metabolomics experiments are different from other types of "-omics" data. For example, a common phenomenon in mass spectrometry (MS)-based metabolomics data is that the data matrix frequently contains missing values, which complicates some quantitative analyses. One way to tackle this problem is to treat them as absent. Hence there are two types of information that are available in metabolomics data: presence/absence of a metabolite and a quantitative value of the abundance level of a metabolite if it is present. Combining these two layers of information poses challenges to the application of traditional statistical approaches in differential expression analysis.
RESULTS
In this article, we propose a novel kernel-based score test for the metabolomics differential expression analysis. In order to simultaneously capture both the continuous pattern and discrete pattern in metabolomics data, two new kinds of kernels are designed. One is the distance-based kernel and the other is the stratified kernel. While we initially describe the procedures in the case of single-metabolite analysis, we extend the methods to handle metabolite sets as well.
CONCLUSIONS
Evaluation based on both simulated data and real data from a liver cancer metabolomics study indicates that our kernel method has a better performance than some existing alternatives. An implementation of the proposed kernel method in the R statistical computing environment is available at http://works.bepress.com/debashis_ghosh/60/ .
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