Version Compatibility

Reference examples tested with: pandas 2.2+, DESeq2 1.42+, edgeR 4.0+, limma 3.58+, variancePartition / dream 1.32+, somalier 0.2.18+ (CLI), pyensembl 2.3+, anndata 0.10+

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

• R: packageVersion('<pkg>') then ?function_name to verify parameters
• Python: pip show <package> then help(module.function) to check signatures
• CLI: <tool> --version then <tool> --help to confirm flags

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

Metadata Joins

"Align my sample metadata with my count matrix and build a design" -> Reconcile sample identifiers, validate the join, set factor levels explicitly to control fold-change direction, encode the experimental structure (paired, repeated measures, interaction) in the design formula, and detect swaps before downstream DE.

The Single Most Important Modern Insight -- Alphabetical reference levels invert fold changes silently

DESeq2 picks the reference level alphabetically if not told otherwise. With condition = c('Treated', 'Untreated'), T < U, so Treated becomes the reference. The reported log2FoldChange is then Untreated vs Treated -- the opposite of what the methods section says. No error; the volcano plot looks plausible; the gene list is correct but with reversed sign.