Analysis of high-dimensional metabolomics data with complex temporal dynamics using RM-ASCA
Copyright: © 2023 Erdős et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited..
The intricate dependency structure of biological "omics" data, particularly those originating from longitudinal intervention studies with frequently sampled repeated measurements renders the analysis of such data challenging. The high-dimensionality, inter-relatedness of multiple outcomes, and heterogeneity in the studied systems all add to the difficulty in deriving meaningful information. In addition, the subtle differences in dynamics often deemed meaningful in nutritional intervention studies can be particularly challenging to quantify. In this work we demonstrate the use of quantitative longitudinal models within the repeated-measures ANOVA simultaneous component analysis+ (RM-ASCA+) framework to capture the dynamics in frequently sampled longitudinal data with multivariate outcomes. We illustrate the use of linear mixed models with polynomial and spline basis expansion of the time variable within RM-ASCA+ in order to quantify non-linear dynamics in a simulation study as well as in a metabolomics data set. We show that the proposed approach presents a convenient and interpretable way to systematically quantify and summarize multivariate outcomes in longitudinal studies while accounting for proper within subject dependency structures.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:19 |
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| Enthalten in: |
PLoS computational biology - 19(2023), 6 vom: 23. Juni, Seite e1011221 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Erdős, Balázs [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 10.07.2023 Date Revised 18.07.2023 published: Electronic-eCollection Citation Status MEDLINE |
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| doi: |
10.1371/journal.pcbi.1011221 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM358537428 |
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| 520 | |a Copyright: © 2023 Erdős et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. | ||
| 520 | |a The intricate dependency structure of biological "omics" data, particularly those originating from longitudinal intervention studies with frequently sampled repeated measurements renders the analysis of such data challenging. The high-dimensionality, inter-relatedness of multiple outcomes, and heterogeneity in the studied systems all add to the difficulty in deriving meaningful information. In addition, the subtle differences in dynamics often deemed meaningful in nutritional intervention studies can be particularly challenging to quantify. In this work we demonstrate the use of quantitative longitudinal models within the repeated-measures ANOVA simultaneous component analysis+ (RM-ASCA+) framework to capture the dynamics in frequently sampled longitudinal data with multivariate outcomes. We illustrate the use of linear mixed models with polynomial and spline basis expansion of the time variable within RM-ASCA+ in order to quantify non-linear dynamics in a simulation study as well as in a metabolomics data set. We show that the proposed approach presents a convenient and interpretable way to systematically quantify and summarize multivariate outcomes in longitudinal studies while accounting for proper within subject dependency structures | ||
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| 700 | 1 | |a Westerhuis, Johan A |e verfasserin |4 aut | |
| 700 | 1 | |a Adriaens, Michiel E |e verfasserin |4 aut | |
| 700 | 1 | |a O'Donovan, Shauna D |e verfasserin |4 aut | |
| 700 | 1 | |a Xie, Ren |e verfasserin |4 aut | |
| 700 | 1 | |a Singh-Povel, Cécile M |e verfasserin |4 aut | |
| 700 | 1 | |a Smilde, Age K |e verfasserin |4 aut | |
| 700 | 1 | |a Arts, Ilja C W |e verfasserin |4 aut | |
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