This tutorial is still under construction

Tutorial 5: Differential Expression (DE)

Run DE analysis at the protein or peptide level. — test across groups (mean, pairwise, peptide-level).

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Protein-Level DE

de_results = pdata.de(group1="treated", group2="control", on="protein")
de_results.head()

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Fold Change Strategies

# Mean-based fold change
pdata.de(group1="treated", group2="control", method="mean")

# Pairwise protein-level median
pdata.de(group1="treated", group2="control", method="protein_pairwise")

# Peptide-level median (via RS matrix)
pdata.de(group1="treated", group2="control", method="peptide_pairwise")

💡 Different strategies may be useful depending on noise and sample size.