FCS Handling - Usage Guide

FCS Handling - Usage Guide

Overview

FCS (Flow Cytometry Standard) is the standard file format for cytometry data. flowCore provides comprehensive tools for reading, writing, and manipulating FCS files.

Prerequisites

# R/Bioconductor
BiocManager::install('flowCore')

Quick Start

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"

Example Prompts

Reading Data

"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"

Writing Data

"Save this flowFrame as a new FCS file" "Export my gated population to a new FCS file"

Metadata

"Show me the acquisition keywords from this FCS file" "Rename the channels to match my antibody panel" "Add sample metadata to my flowSet"

What the Agent Will Do

1. Load flowCore library
2. Read FCS files with appropriate settings (transformation=FALSE, truncate_max_range=FALSE)
3. Create flowFrame (single file) or flowSet (multiple files) objects
4. Extract expression matrices and parameter metadata as needed
5. Optionally rename channels or add sample annotations

Tips

• Use transformation=FALSE to get raw data without default transformations
• Use truncate_max_range=FALSE to 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

Key Objects

Common Parameters

References

• FCS specification: https://isac-net.org/
• flowCore: doi:10.1186/1471-2105-10-106