Figure 1.

Flowchart of the analysis pipeline. Flowchart describing our analysis pipeline. a) Procedure for analyzing FSC vs SSC channels. Standard data analysis procedures are depicted by path 1, whereas procedures applying parameter-optimized transformations are depicted by path 2. b) Procedure for analyzing fluorescence channels. Standard procedures are depicted by path 1). Procedures utilizing optimized transformations are depicted by path 2. The default transformation depicted in 1) is the generalized arcsinh with default parameters (a = 1, b = 1, c = 0), as defined in the flowCore package. Normalization follows transformation in b) to ensure that the transformed data are on a common scale.