Metabolomics Navigator Tools, strategies & workflow guidance for metabolomics

Normalization and batch correction

CordBat

An R package implementing concordance-based batch-effect correction for large-scale metabolomics studies.

Platform-independentMetabolite profilingR packageOpen source
Access toolSuggest an update

Overview

CordBat implements concordance-based correction of batch effects in quantified metabolomics matrices. Its R interface takes batch and biological-group information and a selected reference batch, returning corrected measurements for further analysis.

What can this tool do?

Batch-effect correction

Common uses

  • Correct batch effects in large metabolomics datasets while preserving concordance structure.

Scientific fit

Primary function

Normalization and batch correction

Analysis types

Metabolite profiling

Data compatibility

Inputs

Feature or peak table, Sample metadata

Outputs

Feature or peak table

Input formats

R abundance matrix with batch/group vectors and reference-batch identifier

Output formats

Corrected R abundance matrix and fitted correction results

Scope and considerations

Designed for

  • An R package implementing concordance-based batch-effect correction for large-scale metabolomics studies.

Not designed for

  • Raw feature extraction or reliable separation of biological and technical effects in an unidentifiable, fully confounded design.

Important requirements

  • R, an appropriately transformed numeric sample-by-feature matrix, batch labels and the biological grouping/reference-batch information expected by the documented function.

Considerations

  • Check matrix orientation and transformation, reference-batch choice and preservation of biological contrasts. A better batch-mixing plot alone does not establish a scientifically valid correction.

Access and documentation

Primary accessDocumentation

Package DESCRIPTION, LICENSE and LICENSE.md specify MIT terms; this R implementation is distinguished from the original method publication.

License: MIT

Evidence and review

Enveda intake rechecked against official repository documentation, package/license metadata and primary publication identity on 2026-10-27. Editorial source review only; no software execution or independent benchmark. See docs/enveda-expansion-review-2026-10-27-batch2.md.

Core publications

Resource papers, direct updates and tool-specific methods. Selection policy.

  1. Concordance-Based Batch Effect Correction for Large-Scale Metabolomics. Analytical Chemistry (2023). doi:10.1021/acs.analchem.2c05748

Related tools

hRUVSimilar function · An R package for hierarchical normalization of multi-batch metabolomics studies using intra-batch and inter-batch replicate information to estimate and remove unwanted variation.MultiBaCSimilar function · A Bioconductor R package for batch-effect correction in single-omics and multi-omics datasets, including metabolomics.NOREVASimilar function · Normalize metabolomics data and compare the performance of alternative normalization strategies.Norm-ISWSVRSimilar function · Norm-ISWSVR normalizes metabolomics tables by combining internal-standard correction with support-vector-regression-based adjustment.

Entry history

Changes to this catalogue entry, not the tool's software release history. Acceptance and editorial review are separate.

  1. 2026-10-27 · First committed entry

    Add 24 reviewed Enveda tools in a separate second batch

    View change · Entry at this revision

Full GitHub history