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

name	bulk-rna-seq-batch-correction-with-combat
title	Bulk RNA-seq batch correction with ComBat
description	Bulk RNA-seq batch correction with pyComBat: remove batch effects from merged cohorts, export corrected matrices, and benchmark visualizations.

Bulk RNA-seq batch correction with ComBat

Overview

Apply this skill when a user has multiple bulk expression matrices measured across different batches and needs to harmonise them before downstream analysis. It follows t_bulk_combat.ipynb, w hich demonstrates the pyComBat workflow on ovarian cancer microarray cohorts.

Instructions

1. Import core libraries
   • Load omicverse as ov, anndata, pandas as pd, and matplotlib.pyplot as plt.
   • Call ov.ov_plot_set() (aliased ov.plot_set() in some releases) to align figures with omicverse styling.
2. Load each batch separately
   • Read the prepared pickled matrices (or user-provided expression tables) with pd.read_pickle(...)/pd.read_csv(...).
   • Transpose to gene × sample before wrapping them in anndata.AnnData objects so adata.obs stores sample metadata.
   • Assign a batch column for every cohort (adata.obs['batch'] = '1', '2', ...). Encourage descriptive labels when availa ble.