Table of Contents Author Guidelines
Advances in Bioinformatics
Volume 2009, Article ID 356141, 10 pages
Research Article

Analysis of High-Throughput Flow Cytometry Data Using plateCore

1FDA-Center for Food Safety and Nutrition, HFS-013 5100 Paint Branch Parkway, College Park, MD 20740, USA
2Fred Hutchison Cancer Research Center, M2-B514 P.O. Box 19024 Seattle, WA 98109, USA
3Terry Fox Laboratory, British Columbia Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada V5Z 1L3
4BD Technologies, 21 Davis Dr, Research Triangle Park, NC 27709, USA

Received 2 April 2009; Accepted 21 July 2009

Academic Editor: Matt Wand

Copyright © 2009 Errol Strain et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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. 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. 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. This same data set was also manually analyzed by a cytometry expert using the FlowJo data analysis software package (TreeStar, USA). 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.