Abstract
BackgroundColony formation assay is the gold standard to determine cell reproductive death after treatment with ionizing radiation, applied for different cell lines or in combination with other treatment modalities. Associated linear-quadratic cell survival curves can be calculated with different methods. For easy code exchange and methodological standardisation among collaborating laboratories a software package CFAssay for R (R Core Team, R: A Language and Environment for Statistical Computing, 2014) was established to perform thorough statistical analysis of linear-quadratic cell survival curves after treatment with ionizing radiation and of two-way designs of experiments with chemical treatments only.MethodsCFAssay offers maximum likelihood and related methods by default and the least squares or weighted least squares method can be optionally chosen. A test for comparision of cell survival curves and an ANOVA test for experimental two-way designs are provided.ResultsFor the two presented examples estimated parameters do not differ much between maximum-likelihood and least squares. However the dispersion parameter of the quasi-likelihood method is much more sensitive for statistical variation in the data than the multiple R2 coefficient of determination from the least squares method.ConclusionThe dispersion parameter for goodness of fit and different plot functions in CFAssay help to evaluate experimental data quality. As open source software interlaboratory code sharing between users is facilitated.AvailabilityThe package is available at http://www.bioconductor.org/packages/release/bioc/html/CFAssay.html.
Highlights
Colony formation assay is the gold standard to determine cell reproductive death after treatment with ionizing radiation, applied for different cell lines or in combination with other treatment modalities
In spite of statistical significance, a critical limit for the dispersion parameter depends on experience and may vary between different labs
Fixed plating efficiencies, derived by option PEmethod = “fix” in the function cellsurvLQfit result in almost identical coefficients but the dispersion parameter of the maximum likelihood (ML) method becomes 9.73
Summary
Colony formation assay is the gold standard to determine cell reproductive death after treatment with ionizing radiation, applied for different cell lines or in combination with other treatment modalities. For easy code exchange and methodological standardisation among collaborating laboratories a software package CFAssay for R (R Core Team, R: A Language and Environment for Statistical Computing, 2014) was established to perform thorough statistical analysis of linear-quadratic cell survival curves after treatment with ionizing radiation and of two-way designs of experiments with chemical treatments only. Whereby the relationship between the radiation doses and the proportion of surviving colonies is usually described by parametric cell survival curves These can be used for the characterisation of the radiation sensitivity of different tumour cell lines given a specific radiation type [2], or in combination with other treatment modalities, e.g. a therapeutic agent or radiation sensitizer [3]. In CFAssay ANOVA based tests are used for two-way designs
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