bulk-rna-seq-batch-correction-with-combat

Remove batch effects from bulk RNA-seq/microarray cohorts using pyComBat, export corrected matrices, and visualize pre/post correction results.

• Harmonize bulk expression data across batches
• Correct for batch effects using pyComBat
• Export raw and corrected expression matrices
• Benchmark correction with visualizations

• Uses omicverse's pyComBat wrapper
• Corrects batch effects in merged cohorts
• Stores corrected values in layers
• Supports both RNA-seq and microarray data
• Exports raw and corrected matrices
• Includes PCA benchmarking for validation
• Requires log-scale intensities or similarly distributed counts
• Mismatches in gene identifiers cause feature drops

1. 1.Import core libraries and set plot styling
2. 2.Load and transpose batch data into AnnData objects with batch metadata
3. 3.Concatenate on shared genes and verify balanced sample counts
4. 4.Run pyComBat batch correction and extract corrected matrices
5. 5.Export raw and corrected data as CSV and H5AD files
6. 6.Visualize before/after PCA embeddings to validate correction