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SelectBCM tool: a batch evaluation framework to select the most appropriate batch-correction methods for bulk

Madhulika Mishra1,2, Lucas Barck1,3,2, Pablo Moreno1,2

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

NAR Genomics and Bioinformatics
|March 7, 2023
PubMed
Summary
This summary is machine-generated.

Integrating bulk transcriptomic data is challenging due to batch effects. The SelectBCM tool helps choose the best batch-correction method, improving biological analysis for diseases like rheumatoid arthritis and osteoarthritis.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Bulk transcriptomes are crucial for biological and disease research.
  • Integrating data from different experiments is difficult due to batch effects caused by technological and biological variations.
  • Existing batch-correction methods lack a user-friendly workflow for selecting the most appropriate approach.

Purpose of the Study:

  • To introduce SelectBCM, a novel tool for prioritizing batch-correction methods in bulk transcriptomic data.
  • To enhance biological clustering and differential gene expression analysis through effective batch correction.
  • To provide a user-friendly workflow for selecting the optimal batch-correction strategy.

Main Methods:

  • Development of the SelectBCM tool, an R package.
  • Prioritization of batch-correction methods based on data characteristics.
  • Demonstration of SelectBCM's applicability on real-world datasets.

Main Results:

  • SelectBCM effectively prioritizes batch-correction methods for bulk transcriptomic experiments.
  • The tool improves biological clustering and gene differential expression analysis.
  • Successful application on datasets related to rheumatoid arthritis, osteoarthritis, and macrophage activation.

Conclusions:

  • SelectBCM addresses the need for a streamlined approach to batch-correction method selection.
  • The tool enhances the reliability and interpretability of integrated bulk transcriptomic data.
  • SelectBCM facilitates more accurate biological insights from diverse transcriptomic studies.