title: FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data.
abstract: The number of markers measured in both flow and mass cytometry keeps increasing steadily. Although this provides a wealth of information, it becomes infeasible to analyze these datasets manually. When using 2D scatter plots, the number of possible plots increases exponentially with the number of markers and therefore, relevant information that is present in the data might be missed. In this article, we introduce a new visualization technique, called FlowSOM, which analyzes Flow or mass cytometry data using a Self-Organizing Map. Using a two-level clustering and star charts, our algorithm helps to obtain a clear overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. R code is available at https://github.com/SofieVG/FlowSOM and will be made available at Bioconductor.
authors.affiliation: Department of Information Technology, Ghent University, iMinds, Ghent, Belgium.|Inflammation Research Center, VIB, Ghent, Belgium.|Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.
authors.forename: Sofie
authors.initials: S
authors.lastname: Van Gassen
authors.affiliation: Department of Information Technology, Ghent University, iMinds, Ghent, Belgium.
authors.forename: Britt
authors.initials: B
authors.lastname: Callebaut
authors.affiliation: Inflammation Research Center, VIB, Ghent, Belgium.|Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.
authors.forename: Mary J
authors.initials: MJ
authors.lastname: Van Helden
authors.affiliation: Inflammation Research Center, VIB, Ghent, Belgium.|Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.
authors.forename: Bart N
authors.initials: BN
authors.lastname: Lambrecht
authors.affiliation: Department of Information Technology, Ghent University, iMinds, Ghent, Belgium.
authors.forename: Piet
authors.initials: P
authors.lastname: Demeester
authors.affiliation: Department of Information Technology, Ghent University, iMinds, Ghent, Belgium.
authors.forename: Tom
authors.initials: T
authors.lastname: Dhaene
authors.affiliation: Inflammation Research Center, VIB, Ghent, Belgium.|Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.
authors.forename: Yvan
authors.initials: Y
authors.lastname: Saeys
mesh_terms: D000465:Algorithms; D015415:Biomarkers / Q000032:analysis; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D005434:Flow Cytometry / Q000379:methods*; D006086:Graft vs Host Disease / Q000175:diagnosis; D018380:Hematopoietic Stem Cell Transplantation; D006801:Humans; D016393:Lymphoma, B-Cell / Q000175:diagnosis; D014901:West Nile Fever / Q000175:diagnosis
chemical_list: D015415:Biomarkers
keywords: Key terms: polychromatic flow cytometry; bioinformatics; exploratory data analysis; mass cytometry; self-organizing map; visualization method