Bulk RNA-seq batch correction with ComBat

What problem does it solves? Combining bulk RNA-seq or microarray data from multiple experiments often introduces technical batch effects that can obscure biological signals. This Skill automates the ComBat batch correction process to harmonize datasets, ensuring more reliable downstream analyses.

Core Features & Use Cases

• Data Merging: Concatenate multiple bulk expression matrices from different batches into a unified dataset.
• ComBat Batch Correction: Apply the ComBat algorithm to effectively remove technical batch effects.
• Matrix Export: Export both the raw and batch-corrected expression matrices for transparency and further use.
• Correction Benchmarking: Visualize PCA embeddings before and after correction to assess the effectiveness of batch removal.
• Use Case: Integrate three independent microarray datasets of ovarian cancer, apply ComBat to remove batch effects, and then visualize the PCA plots to confirm successful harmonization before downstream analysis.

Quick Start

Combine my three bulk RNA-seq batches, apply ComBat correction, and show PCA plots before and after to confirm batch removal.