Loading...
Please wait, while we are loading the content...
Similar Documents
NMF-Based Approach for Missing Values Imputation of Mass Spectrometry Metabolomics Data
| Content Provider | MDPI |
|---|---|
| Author | Xu, Jingjing Wang, Yuanshan Xu, Xiangnan Cheng, Kian-Kai Raftery, Daniel Dong, Jiyang |
| Copyright Year | 2021 |
| Description | In mass spectrometry (MS)-based metabolomics, missing values (NAs) may be due to different causes, including sample heterogeneity, ion suppression, spectral overlap, inappropriate data processing, and instrumental errors. Although a number of methodologies have been applied to handle NAs, NA imputation remains a challenging problem. Here, we propose a non-negative matrix factorization (NMF)-based method for NA imputation in MS-based metabolomics data, which makes use of both global and local information of the data. The proposed method was compared with three commonly used methods: k-nearest neighbors (kNN), random forest (RF), and outlier-robust (ORI) missing values imputation. These methods were evaluated from the perspectives of accuracy of imputation, retrieval of data structures, and rank of imputation superiority. The experimental results showed that the NMF-based method is well-adapted to various cases of data missingness and the presence of outliers in MS-based metabolic profiles. It outperformed kNN and ORI and showed results comparable with the RF method. Furthermore, the NMF method is more robust and less susceptible to outliers as compared with the RF method. The proposed NMF-based scheme may serve as an alternative NA imputation method which may facilitate biological interpretations of metabolomics data. |
| Starting Page | 5787 |
| e-ISSN | 14203049 |
| DOI | 10.3390/molecules26195787 |
| Journal | Molecules |
| Issue Number | 19 |
| Volume Number | 26 |
| Language | English |
| Publisher | MDPI |
| Publisher Date | 2021-09-24 |
| Access Restriction | Open |
| Subject Keyword | Molecules Biochemical Research Non-negative Matrix Factorization Missing Values Imputation Mass Spectrometry Metabolomics Data Missing Pattern Outliers |
| Content Type | Text |
| Resource Type | Article |
