Version Compatibility

Reference examples tested with: MSnbase 2.28+, scanpy 1.10+, 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.

XCMS Metabolomics Preprocessing

Requires Bioconductor 3.18+ with xcms 4.0+ and MSnbase 2.28+.

Load Raw Data

Goal: Import raw LC-MS files into R for downstream peak detection and alignment.

Approach: Read mzML/mzXML files into an OnDiskMSnExp object using MSnbase for memory-efficient access.