Alternative Approaches for Analysis of Complex Data Sets in Flow Cytometry

The field of flow cytometry is rapidly evolving as a result of advancements in sample preparation technology. Automated machinery, multi-channel PMTs, multiplexed assay formats, and mass cytometry introduce new opportunities in fields utilizing flow cytometry by creating very rich, albeit complex, data sets. Advances in cytometric data collection have always been accompanied by advances in analytical techniques. As high-content multi-parametric data sets are generated through new flow cytometry techniques and technologies, it is important to simultaneously develop computers and software with the ability to execute six major functions: manipulate an unlimited number of parameters, compare all data parameters in many different combinations, create and customize a data analysis strategy, see real-time changes in all parameters, offer advanced statistical tools, and rapidly report figures and graphs with endpoint conclusions. This chapter investigates methods of achieving each of these six functions by addressing data-analysis challenges in drug-screen assays, multiplexed cytokine assays, hyperspectral cytometry, and mass cytometry.