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Usually one compares the accuracy of two competing classifiers using null hypothesis significance tests. Yet such tests suffer from important shortcomings, which can be overcome by switching to Bayesian hypothesis testing. We propose a Bayesian hierarchical model that jointly analyzes the cross-validation results obtained by two classifiers on multiple data sets. The model estimates more accurately the difference between classifiers on the individual data sets than the traditional approach of averaging, independently on each data set, the cross-validation results. It does so by jointly analyzing the results obtained on all data sets, and applying shrinkage to the estimates. The model eventually returns the posterior probability of the accuracies of the two classifiers being practically equivalent or significantly different.