The statistical performance of an MCF‐7 cell culture assay evaluated using generalized linear mixed models and a score test

Abstract

Biological assays often utilize experimental designs where observations are replicated at multiple levels, and where each level represents a separate component of the assay's overall variance. Statistical analysis of such data usually ignores these design effects, whereas more sophisticated methods would improve the statistical power of assays. This report evaluates the statistical performance of an in vitro MCF-7 cell proliferation assay (E-SCREEN) by identifying the optimal generalized linear mixed model (GLMM) that accurately represents the assay's experimental design and variance components. Our statistical assessment found that 17beta-oestradiol cell culture assay data were best modelled with a GLMM configured with a reciprocal link function, a gamma error distribution, and three sources of design variation: plate-to-plate; well-to-well, and the interaction between plate-to-plate variation and dose. The gamma-distributed random error of the assay was estimated to have a coefficient of variation (COV) = 3.2 per cent, and a variance component score test described by X. Lin found that each of the three variance components were statistically significant. The optimal GLMM also confirmed the estrogenicity of five weakly oestrogenic polychlorinated biphenyls (PCBs 17, 49, 66, 74, and 128). Based on information criteria, the optimal gamma GLMM consistently out-performed equivalent naive normal and log-normal linear models, both with and without random effects terms. Because the gamma GLMM was by far the best model on conceptual and empirical grounds, and requires only trivially more effort to use, we encourage its use and suggest that naive models be avoided when possible.