Comparative analysis of dimension reduction methods for cytometry by time-of-flight data

While experimental and informatic techniques around single cell sequencing (scRNA-seq) are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged behind. CyTOF data are notably different from scRNA-seq data in many aspects. This calls for the evaluation and development of...

Full description

Saved in:
Bibliographic Details
Published in:Nature communications 2023-04, Vol.14 (1), p.1836-1836, Article 1836
Main Authors: Wang, Kaiwen, Yang, Yuqiu, Wu, Fangjiang, Song, Bing, Wang, Xinlei, Wang, Tao
Format: Article
Language:English
Subjects:
631/114/1767
631/114/2416
631/114/794
631/1647/1407
631/250
82/80
Algorithms
Benchmarks
Cluster Analysis
Comparative analysis
Complementarity
Computer applications
Cytometry
Data analysis
Data structures
Gene Expression Profiling - methods
Humanities and Social Sciences
multidisciplinary
Preservation
Reduction
Science
Science (multidisciplinary)
Sequence Analysis, RNA - methods
Single-Cell Analysis - methods
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:While experimental and informatic techniques around single cell sequencing (scRNA-seq) are advanced, research around mass cytometry (CyTOF) data analysis has severely lagged behind. CyTOF data are notably different from scRNA-seq data in many aspects. This calls for the evaluation and development of computational methods specific for CyTOF data. Dimension reduction (DR) is one of the critical steps of single cell data analysis. Here, we benchmark the performances of 21 DR methods on 110 real and 425 synthetic CyTOF samples. We find that less well-known methods like SAUCIE, SQuaD-MDS, and scvis are the overall best performers. In particular, SAUCIE and scvis are well balanced, SQuaD-MDS excels at structure preservation, whereas UMAP has great downstream analysis performance. We also find that t-SNE (along with SQuad-MDS/t-SNE Hybrid) possesses the best local structure preservation. Nevertheless, there is a high level of complementarity between these tools, so the choice of method should depend on the underlying data structure and the analytical needs. Dimension reduction (DR) is a key step of Cytometry by Time-of-Flight (CyTOF) data analysis. Here, the authors benchmark 21 DR methods on 110 real and 425 synthetic CyTOF samples, finding a high level of complementarity between the methods, and providing a comprehensive set of user guidelines.
ISSN:2041-1723
2041-1723
DOI:10.1038/s41467-023-37478-w