Quantitative Issues in Cancer Research Working Seminar

Jill Lundell, Ph.D.
Research Fellow, Department of Biostatistics, Harvard T.H. Chan School of Public Health

“Where did all of my tumor cells go? A better way to clean CyTOF data using cytofQC.”

ABSTRACT: Cytometry by time of flight, or CyTOF, is a powerful alternative to flow cytometry for quantifying targets on the surface and interior of cells. CyTOF data requires considerable cleaning because many observations are debris, doublets, or calibration beads. As with any technology, the data analysis is only as good as the data itself so careful data cleaning is essential. One of the biggest data cleaning challenges is dealing with doublets because it is difficult to distinguish between large cells and doublets. I will introduce an R package, cytofQC, that uses a modeling and labeling approach to data cleaning that allows for more careful and customized cleaning of CyTOF data.