Version Compatibility

Reference examples tested with: xcms 4.0+

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Metabolomics Normalization and QC

Load and Inspect Data

Goal: Load the feature table and sample metadata, separating QC and biological samples for downstream processing.

Approach: Read CSV files, partition by sample type, and assess missing value prevalence.

"Normalize my metabolomics data and correct for batch effects" → Apply QC-based signal correction, handle missing values, transform intensities, and assess normalization quality via RSD and PCA.