Version Compatibility

Reference examples tested with: limma 3.58+

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.

Batch Design and Mitigation

"Design experiment to avoid batch effects" → Plan sample-to-batch assignments that confound biology with technical variation, and apply correction methods post-hoc.

• R: sva::ComBat(), limma::removeBatchEffect()
• Python: scanpy.pp.combat() for single-cell data

Core Principle

Batch effects are unavoidable. Good design makes them correctable.