6 Gating Data

6.1 The Essentials

1. Gate your files to exclude doublets and dead cells with a software package like FlowJo or Cytobank
2. Export new fcs files that only include the Live, Single events

For data analysis it’s essential to remove any confounding or extraneous events. In cytometry this means getting rid of dead cells and doublets. For high parameter analysis this is doubly important. The analysis is computationally taxing so removing this data helps speed up the analysis as well as improving the quality.

It is much simpler to manual gate in a graphical user interface like FlowJo or Cytobank than to gate with the R command line.

6.2 A Deeper Dive

I highly recommend you learn to gate and export selected events in FlowJo or Cytobank. What follows here is a demonstration of what is possible with R rather than a recommendation of how handle your own data.