FCS (Flow Cytometry Standard) is the standard file format for cytometry data. flowCore provides comprehensive tools for reading, writing, and manipulating FCS files.
# R/Bioconductor
BiocManager::install('flowCore')Tell your AI agent what you want to do:
- "Read my FCS files into R for analysis"
- "Combine multiple FCS files into a flowSet"
- "Extract the expression matrix from this FCS file"
"Load all FCS files from this directory into a flowSet" "Read this FCS file and show me the channel names" "Extract raw expression data without any transformation"
"Save this flowFrame as a new FCS file" "Export my gated population to a new FCS file"
"Show me the acquisition keywords from this FCS file" "Rename the channels to match my antibody panel" "Add sample metadata to my flowSet"
- Load flowCore library
- Read FCS files with appropriate settings (transformation=FALSE, truncate_max_range=FALSE)
- Create flowFrame (single file) or flowSet (multiple files) objects
- Extract expression matrices and parameter metadata as needed
- Optionally rename channels or add sample annotations
- Use
transformation=FALSEto get raw data without default transformations - Use
truncate_max_range=FALSEto preserve values beyond detector range - flowFrame = single FCS file, flowSet = collection of samples
- -A (Area) parameters are most common, -H (Height) and -W (Width) are for doublet detection
- Check the Time parameter for acquisition issues
| Object | Description |
|---|---|
| flowFrame | Single FCS file with expression matrix + metadata |
| flowSet | Collection of flowFrames with shared pData |
| Type | Examples |
|---|---|
| Scatter | FSC-A, FSC-H, SSC-A, SSC-H |
| Time | Time |
| Fluorescence | FL1-A, FITC-A, PE-A |
| Mass (CyTOF) | Ir191Di, Yb176Di |
- FCS specification: https://isac-net.org/
- flowCore: doi:10.1186/1471-2105-10-106