Version Compatibility

Reference examples tested with: DESeq2 1.42+, edgeR 4.0+, ggplot2 3.5+, pheatmap 1.0+, matplotlib 3.8+, numpy 1.26+, pandas 2.2+, scikit-learn 1.4+, scipy 1.12+, seaborn 0.13+

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

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

Count Matrix QC

"Check my count matrix for outliers and batch effects" -> Assess depth, composition, sample relationships, and outliers on appropriately transformed data, then decide what (if anything) to remove or model before differential expression.

• R: DESeq2::vst() -> plotPCA(), sample-distance heatmap, Cook's distance
• Python: sklearn.decomposition.PCA, seaborn.clustermap (with the low-count caveat below)

Two principles govern this whole skill. First, DE testing runs on raw counts with a size-factor offset; the transformed matrices here are for QC and visualization only, never fed back into the count model. Second, raw counts confound depth, composition, and biology, so QC must look at the right scale: a variance-stabilized matrix for clustering/PCA, and the size factors and Cook's distances from the count model for normalization and outliers.