sweetD: An R package using Hoeffding’s D statistic to visualise the dependence between M and A for large numbers of gene expression samples

Summary MA plots are frequently used to examine the relationship between gene abundance and differences in gene expression between two samples. In good quality samples without batch effects or outliers, there is generally no or little relationship between intensity and log fold difference. As the number of MA plots increases quadratically with the number of samples, for large datasets the number of potential MA plots becomes prohibitively high for manual examination. Here we present an R package calculating and visualising the dependence between abundance and log fold difference for large numbers of samples using Hoeffding’s D statistic. Availability and implementation sweetD is currently available as an R package on Github https://github.com/amberjoybarton/sweetD .