Simulation-based comprehensive study of batch effects in metabolomics studies
Bibliographic record
Abstract
Abstract Batch effects will influence the interpretation of metabolomics data. In order to avoid misleading results, batch effects should be corrected and normalized prior to statistical analysis. Metabolomics studies are usually performed without targeted compounds (e.g., internal standards) and it is a challenging task to validate batch effects correction methods. In addition, statistical properties of metabolomics data are quite different from genomics data (where most of the currently used batch correction methods have originated from). In this study, we firstly analyzed already published metabolomics datasets so as to summarize and discuss their statistical properties. Then, based on available datasets, we developed novel statistical properties-based in silico simulations of metabolomics peaks’ intensity data so as to analyze the influence of batch effects on metabolomic data with the use of currently available batch correction strategies. Overall, 252000 batch corrections on 14000 different in silico simulated datasets and related differential analyses were performed in order to evaluate and validate various batch correction methods. The obtained results indicate that log transformations strongly influence the performance of all investigated batch correction methods. False positive rates increased after application of batch correction methods with almost no improvement on true positive rates among the analyzed batch correction methods. Hence, in metabolomic studies it is recommended to implement preliminary experiments to simulate batch effects from real data in order to select adequate batch correction method, based on a given distribution of peaks intensity. The presented study is reproducible and related R package mzrtsim software can be found online ( https://github.com/yufree/mzrtsim ).
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.004 | 0.008 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.002 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".