DE-AoP: Data & Analyses

Data and R code for the DE-AoP project and paper

RT-qPCR and immunohistochemistry data for the DE-AoP project were analysed in R, hosted on GitHub, and archived through Zenodo.

Marc-Aurèle Rivière


July 13, 2023


The DE-AoP project included RT-qPCR and immunohistochemistry data, which were analysed in R (R Core Team, 2023). Data were modeled through the Generalized Linear Mixed Model (GLMM) framework, using the glmmTMB package (Brooks et al., 2017). Random intercepts were added to account for the correlation between pseudo-replicates. Temporally-dependent repeated measures were modeled using auto-regressive (AR1) terms.

The optimal likelihood families were selected based on our theoretical understanding of the variable’s properties, and to minimize Aikake’s Information Criterion (AIC). Count data (e.g., cell counts, number of maze entries, …) were modeled using a Generalized Poisson likelihood, measures bound at 0 (e.g., cell density, volumes, weights, …) were modeled using a Gamma likelihood, and proportions (e.g., ratios of areas) with a Beta likelihood.

Model diagnostics were done using the DHARMa (Hartig, 2022) & performance (Lüdecke et al., 2021) packages, and estimated marginal means/contrasts were computed with the emmeans package (Lenth, 2022).

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Brooks, M. E., Kristensen, K., van Benthem, K. J., Magnusson, A., Berg, C. W., Nielsen, A., Skaug, H. J., Maechler, M., & Bolker, B. M. (2017). glmmTMB balances speed and flexibility among packages for zero-inflated generalized linear mixed modeling. The R Journal, 9(2), 378–400.
Hartig, F. (2022). DHARMa: Residual diagnostics for hierarchical (multi-level / mixed) regression models.
Lenth, R. V. (2022). Emmeans: Estimated marginal means, aka least-squares means.
Lüdecke, D., Ben-Shachar, M. S., Patil, I., Waggoner, P., & Makowski, D. (2021). performance: An R package for assessment, comparison and testing of statistical models. Journal of Open Source Software, 6(60), 3139.
R Core Team. (2023). R: A language and environment for statistical computing. R Foundation for Statistical Computing.
Circular plot illustrating the impact of the multiple genes tested on several key biological pathways