This code is an R script that can be used to analyze flow cytometry data for both the Broad and Koch Institute flow cytometers. It performs a series of gating steps to identify cells of interest and generates plots/spreadsheets to quantify the reporter protein expression.
To run the code, you need to have R and the following libraries installed: flowCore, flowWorkspace, ggcyto, knitr, dplyr, and broom.
- Choose the correct script to run based on the instrument used
- Open the R console and set the working directory to the location of the script.
- Modify the directory path in the code to specify the location of the fcs files.
- Run the script.
- The script will generate a CSV file and several plots, which will be saved as pdf files in the same directory.
The script outputs several plots and a CSV file containing fluorescence and gating statistics, with the number and percentage of cells in relevant gates. The plots show gates and the expression of the constitutive reporter gene in each sample.
The coordinates of the gating polygons and the reporter gene expression range should be adjusted based on the data being analyzed. These parameters are specified in the comments in the code and should be modified according to the user's needs.