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RUCova: Removal of unwanted covariance in mass cytometry data.
Bioinformatics 40:btae669 (2024)
MOTIVATION: High dimensional single-cell mass cytometry data are confounded by unwanted covariance due to variations in cell size and staining efficiency, making analysis and interpretation challenging. RESULTS: We present RUCova, a novel method designed to address confounding factors in mass cytometry data. RUCova removes unwanted covariance from measured markers applying multivariate linear regression based on Surrogates of sources Unwanted Covariance (SUCs) and principal component analysis (PCA). We exemplify the use of RUCova and show that it effectively removes unwanted covariance while preserving genuine biological signals. Our results demonstrate the efficacy of RUCova in elucidating complex data patterns, facilitating the identification of activated signalling pathways, and improving the classification of important cell populations such as apoptotic cells. By providing a robust framework for data normalization and interpretation, RUCova enhances the accuracy and reliability of mass cytometry analyses, contributing to advances in our understanding of cellular biology and disease mechanisms. AVAILABILITY AND IMPLEMENTATION: The R package is available on https://github.com/molsysbio/RUCova. Detailed documentation, data, and the code required to reproduce the results are available on https://doi.org/10.5281/zenodo.10913464. SUPPLEMENTARY INFORMATION: Available at Bioinformatics online (PDF).
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Publication type
Article: Journal article
Document type
Scientific Article
Keywords
R Package ; Cell Size ; Covariance ; Mass Cytometry; Morphological-changes; Control Genes; Apoptosis
ISSN (print) / ISBN
1367-4803
e-ISSN
1367-4811
Journal
Bioinformatics
Quellenangaben
Volume: 40,
Issue: 11,
Article Number: btae669
Publisher
Oxford University Press
Publishing Place
Oxford
Non-patent literature
Publications
Reviewing status
Peer reviewed
Institute(s)
Translational Metabolic Oncology (IDC-TMO)
Grants
Deutsche Forschungsgemeinschaft (DFG)
Bundesministerium fur Bildung und Forschung (BMBF)
Bundesministerium fur Bildung und Forschung (BMBF)