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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.<\/jats:p>","DOI":"10.1155\/2009\/356141","type":"journal-article","created":{"date-parts":[[2009,10,12]],"date-time":"2009-10-12T07:49:53Z","timestamp":1255333793000},"page":"1-10","source":"Crossref","is-referenced-by-count":9,"title":["Analysis of High-Throughput Flow Cytometry Data Using plateCore"],"prefix":"10.1155","volume":"2009","author":[{"given":"Errol","family":"Strain","sequence":"first","affiliation":[{"name":"FDA-Center for Food Safety and Nutrition, HFS-013 5100 Paint Branch Parkway, College Park, MD 20740, USA"}]},{"given":"Florian","family":"Hahne","sequence":"additional","affiliation":[{"name":"Fred Hutchison Cancer Research Center, M2-B514 P.O. 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