BACKGROUND: The recent development of semiautomated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in the development of high throughput flow cytometry methods for data analysis and display. Especially, data quality control and quality assessment are crucial steps in processing and analyzing high throughput flow cytometry data. METHODS: We propose a variety of graphical exploratory data analytic tools for exploring ungated flow cytometry data. We have implemented a number of specialized functions and methods in the Bioconductor package rflowcyt. We demonstrate the use of these approaches by investigating two independent sets of high throughput flow cytometry data. RESULTS: We found that graphical representations can reveal substantial nonbiological differences in samples. Empirical Cumulative Distribution Function and summary scatterplots were especially useful in the rapid identification of problems not identified by manual review. CONCLUSIONS: Graphical exploratory data analytic tools are quick and useful means of assessing data quality. We propose that the described visualizations should be used as quality assessment tools and where possible, be used for quality control.
BACKGROUND: The recent development of semiautomated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in the development of high throughput flow cytometry methods for data analysis and display. Especially, data quality control and quality assessment are crucial steps in processing and analyzing high throughput flow cytometry data. METHODS: We propose a variety of graphical exploratory data analytic tools for exploring ungated flow cytometry data. We have implemented a number of specialized functions and methods in the Bioconductor package rflowcyt. We demonstrate the use of these approaches by investigating two independent sets of high throughput flow cytometry data. RESULTS: We found that graphical representations can reveal substantial nonbiological differences in samples. Empirical Cumulative Distribution Function and summary scatterplots were especially useful in the rapid identification of problems not identified by manual review. CONCLUSIONS: Graphical exploratory data analytic tools are quick and useful means of assessing data quality. We propose that the described visualizations should be used as quality assessment tools and where possible, be used for quality control.
Authors: Saumyadipta Pyne; Xinli Hu; Kui Wang; Elizabeth Rossin; Tsung-I Lin; Lisa M Maier; Clare Baecher-Allan; Geoffrey J McLachlan; Pablo Tamayo; David A Hafler; Philip L De Jager; Jill P Mesirov Journal: Proc Natl Acad Sci U S A Date: 2009-05-14 Impact factor: 11.205
Authors: Stephen P Perfetto; David Ambrozak; Richard Nguyen; Pratip K Chattopadhyay; Mario Roederer Journal: Nat Protoc Date: 2012-11-08 Impact factor: 13.491
Authors: Kipper Fletez-Brant; Josef Špidlen; Ryan R Brinkman; Mario Roederer; Pratip K Chattopadhyay Journal: Cytometry A Date: 2016-03-18 Impact factor: 4.355