Introduction to using FacsKin

FacsKin is a computer program that enables the mathematical description and statistical comparison of Flow Cytometry acquired kinetic measurements (such as calcium flux measurements). The output of a Flow Cytometry measurement is an FCS file containing FSC, SSC, fluorescent and time parameter values for each cell in the specimen. Kinetic measurements are special because the distribution of at least one parameter (the kinetic parameter) changes as time passes. FacsKin is able to describe the kinetic change that occurs during the measurement by fitting different functions to the kinetic parameter values. By selecting a common function that describes every measurement well, FacsKin is able to compare different groups of measurements based on parameters of the selected function. The available functions and thus the kinetic changes that FacsKin is able to describe are the following (Figure 1):

  • constant: the value of the kinetic parameter is constant during the measurement timeframe
  • logist+: the kinetic parameter starts at a given value, increases during the measurement timeframe and reaches a given value
  • logist-: same as logist+, but the kinetic parameter value is decreasing during the measurement timeframe
  • dlogist+: the kinetic parameter starts at a given value, increases, reaches a maximum value and then decreases and reaches a given value during the measurement timeframe
  • dlogist-: same as dlogist+, but the kinetic parameter value first decreases, reaches a minimum and then increases

The analysis with FacsKin requires the following steps (Figure 2):

  1. Acquiring measurement data
  2. Starting FacsKin
  3. Opening and gating FCS files
  4. Generating a .kinetics file from the gated data in R.
  5. Opening different .kinetics files and selecting a common function (a .kinetics file contains the results of fitting all 5 previously described functions to the gated data)
  6. Creating groups and comparing parameters of the selected function in different groups