Version Compatibility

Reference examples tested with: DESeq2 1.42+, ggplot2 3.5+, limma 3.58+, scanpy 1.10+

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 Effect Correction

ComBat-Seq (Count Data)

Goal: Remove batch effects from raw count data while preserving biological group differences.

Approach: Apply ComBat-Seq's negative binomial regression to adjust counts, keeping the integer nature of the data.

"Remove batch effects from my RNA-seq counts" → Adjust raw count matrix for known batch labels using negative binomial modeling, preserving biological condition effects.