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Interpreting flow cytometry data: a guide for the perplexed

Nature Immunology volume 7, pages 681–685 (2006)Cite this article

Recent advances in flow cytometry technologies are changing how researchers collect, look at and present their data.

Recent advances in fluorescence-activated cell sorting (FACS) technology offer new and exciting approaches for understanding, monitoring and combating immune-related diseases. However, these technological advances also introduce considerable challenges for the producers, reviewers and readers of today's immunology literature. Although some laboratories have readily adopted today's improved FACS data acquisition and analysis methods, too many others have found it difficult to understand how or even believe that using the older methods can lead to serious misinterpretations of FACS data. In essence, results for the same sample can be very different (as described below) depending on whether the data for the sample are collected and displayed with the older or newer methods. In fact, disputes can arise over what might seem to be incompatible data, but the contradictions could simply reflect unrecognized differences in how the data are processed and displayed. These problems and limitations are becoming more apparent and more important as measurement technologies change and as the number of fluorescence labels being routinely measured increases.

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Figure 1: 'Logicle' displays provide improved representation of cells with minimal fluorescence.
Figure 2: 'Logicle' displays are superior to logarithmic displays in determining whether compensation has been properly applied to the sample.
Figure 3: Quantile contour plots provide more accurate data representation than dot plots.

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Authors and Affiliations

  1. Department of Genetics, Stanford University School of Medicine, Stanford, 94305-5318, California, USA

    Leonore A Herzenberg, James Tung, Wayne A Moore, Leonard A Herzenberg & David R Parks

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  1. Leonore A Herzenberg
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  2. James Tung
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  3. Wayne A Moore
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  4. Leonard A Herzenberg
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  5. David R Parks
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Herzenberg, L., Tung, J., Moore, W. et al. Interpreting flow cytometry data: a guide for the perplexed. Nat Immunol 7, 681–685 (2006). https://doi.org/10.1038/ni0706-681

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