Quantitative Comparison of Conventional and t-SNE-guided Gating Analyses
| Autor: | William E. O'Gorman, W. Rodney Mathews, Maclean N. Nyachienga, Sean Lear, Cherie Green, Amelia Au-Yeung, Chikara Takahashi, Shadi Toghi Eshghi, Christopher R. Bolen |
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| Rok vydání: | 2019 |
| Předmět: |
lcsh:Immunologic diseases. Allergy
0301 basic medicine Computer science T-Lymphocytes high-dimensional cytometry Immunology Bivariate analysis Gating Computational biology cytometry informatics Continuous variable Correlation 03 medical and health sciences 0302 clinical medicine Data visualization immunophenotyping cyTOF Humans Immunology and Allergy Mass cytometry Technology Report dimensionality reduction Principal Component Analysis business.industry Dimensionality reduction Flow Cytometry t-SNE 030104 developmental biology Specific immune cell Single-Cell Analysis lcsh:RC581-607 business 030215 immunology |
| Zdroj: | Frontiers in Immunology, Vol 10 (2019) Frontiers in Immunology |
| ISSN: | 1664-3224 |
| DOI: | 10.3389/fimmu.2019.01194 |
| Popis: | Dimensionality reduction using the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm has emerged as a popular tool for visualizing high-parameter single-cell data. While this approach has obvious potential for data visualization it remains unclear how t-SNE analysis compares to conventional manual hand-gating in stratifying and quantitating the frequency of diverse immune cell populations. We applied a comprehensive 38-parameter mass cytometry panel to human blood and compared the frequencies of 28 immune cell subsets using both conventional bivariate and t-SNE-guided manual gating. t-SNE analysis was capable of stratifying every general cellular lineage and most sub-lineages with high correlation between conventional and t-SNE-guided cell frequency calculations. However, specific immune cell subsets delineated by the manual gating of continuous variables were not fully separated in t-SNE space thus causing discrepancies in subset identification and quantification between these analytical approaches. Overall, these studies highlight the consistency between t-SNE and conventional hand-gating in stratifying general immune cell lineages while demonstrating that particular cell subsets defined by conventional manual gating may be intermingled in t-SNE space. |
| Databáze: | OpenAIRE |
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