We will learn how to read and pre-process FCS files using both R and Python. The main components of dealing with FCS files are as follows
- Reading an FCS file
- Applying an Arcsinh transformation
- Getting interpretable marker names that correspond to the antibodies in the experiments
- Subset only the channels of interest (e.g. phenotypic and functional markers)
These examples show you how to create your cells x marker matrices that can be used for downstream tasks.
First, make sure you have FlowKit installed:
pip3 install FlowKitYou can read the following for more info about FlowKit,
You can check out sampleFCSProcess.py to see steps with instructions or,
python3 sampleFCSProcess.pyIt will print a preview of the cell x marker data matrix.
Makre sure you have flowCore installed,
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("flowCore")You can read more about flowCore here,
You can check out flowCoreProcess.R to see steps with instructions or,
source('flowCoreProcess.R')This will print a sample of your data matrix, which is the same as with flowkit :)