Intro:
- Installing R & R studio
- Updating R and packages
- Setting and viewing working directory
- Establishing a file system for your data files and analysis files
- Copying and understanding the script files
Data pre-processing in FlowJo:
- Unzip files
- Use Unmixed files for Aurora
- Import into FlowJo
- Gating
- Use template if you don’t know what you are doing
- Setting groups
- Scaling data
- Exporting populations with names
- Downsampling (Don’t)
- Checking exported files
Importing data into R:
- Copying parameter file
- Editing parameter file
- Group names
- Panel parameters
- Understanding errors in loading data
- Offset error
- Scaling error
- Working directory error
- Typographical error
Running the script:
- Setting the arcsinh transform
- Running FlowSOM
- Running tSNE and UMAP
- Running tSNE-diff
- Altering FlowSOM cluster names
- Altering graphical parameters