Flowjo 10 mfi4/1/2024 Flow Cytometry-High-Content Screening (FC-HCS) experiments generate large volumes of data, which requires a systematic approach to preprocessing, gating (i.e., filtering), and summarizing results for robust analyses. While there are a number of different software packages available for analysis of FCM data, these programs are often ill-suited to the development of new methods needed for analyzing high-throughput FCM studies. We show that the expression values for markers characterized using the automated approach in plateCore are in good agreement with those from FlowJo, and that using plateCore allows for more reproducible analyses of FCM screening data. This same data set was also manually analyzed by a cytometry expert using the FlowJo data analysis software package (TreeStar, USA). plateCore was used to analyze data from a BD FACS CAP screening experiment where five Peripheral Blood Mononucleocyte Cell (PBMC) samples were assayed for 189 different human cell surface markers. We created plateCore, a new package that extends the functionality in these core packages to enable automated negative control-based gating and make the processing and analysis of plate-based data sets from high-throughput FCM screening experiments easier. Flow cytometry (FCM) software packages from R/Bioconductor, such as flowCore and flowViz, serve as an open platform for development of new analysis tools and methods.
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