flowCore framework. For each experiment, the content of the FCS files, phenotypic and metadata are stored in a flowSet. Each flowFrame in a flowSet corresponds to one FCS file. All basic operations (e.g., compensation, transformation, gating) can be applied to either single flowFrames or a flowSet simultaneously.
Hahne et al. BMC Bioinformatics 2009 10:106 doi:10.1186/1471-2105-10-106