Version Compatibility

Reference examples tested with: limma 3.58+, DEqMS 1.20+, ashr 2.2+, proDA 1.20+, numpy 1.26+, pandas 2.2+, scipy 1.12+, statsmodels 0.14+

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

• Python: pip show <package> then help(module.function) to check signatures
• 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.

Differential Protein Abundance

"Find differentially abundant proteins between my conditions" -> Perform statistical testing on protein intensities to identify significant abundance changes.

• R: limma::eBayes() for empirical Bayes moderated t-tests (preferred for small n)
• R: DEqMS::spectraCounteBayes() when PSM/peptide count metadata is available
• R: proDA::test_diff() when missing values are extensive (label-free)
• Python: scipy.stats.ttest_ind(equal_var=False) with statsmodels BH correction