Apr 8, 2016

Comparison of Clustering Methods for High-Dimensional Single-Cell Flow and Mass Cytometry Data

BioRxiv : the Preprint Server for Biology
Lukas M Weber, Mark D Robinson

Abstract

Recent technological developments in high-dimensional flow cytometry and mass cytometry (CyTOF) have made it possible to detect expression levels of dozens of protein markers in thousands of cells per second, allowing cell populations to be characterized in unprecedented detail. Traditional data analysis by "manual gating" can be inefficient and unreliable in these high-dimensional settings, which has led to the development of a large number of automated analysis methods. Methods designed for unsupervised analysis use specialized clustering algorithms to detect and define cell populations for further downstream analysis. Here, we have performed an up-to-date, extensible performance comparison of clustering methods for high-dimensional flow and mass cytometry data. We evaluated methods using several publicly available data sets from experiments in immunology, containing both major and rare cell populations, with cell population identities from expert manual gating as the reference standard. Several methods performed well, including FlowSOM, X-shift, PhenoGraph, Rclusterpp, and flowMeans. Among these, FlowSOM had extremely fast runtimes, making this method well-suited for interactive, exploratory analysis of large, high-dimension...Continue Reading

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Mentioned in this Paper

Flow Cytometry
2-Dimensional
Methyl coenzyme M
Ferric Carboxymaltose Solution
Immunology
Shifted protein, Drosophila
Evaluation
Analysis of Substances
2D Doppler Echocardiography
Analysis

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