model was calculated using a likelihood ratio (LR) test with the D = −2*log(LR) as the test statistic, which can be approximated by a Chi-square distribution with one degree of freedom. The p-values were adjusted for multiple testing by FDR correction [58]. In the replication study the batch effect was omitted from the model due to change of Illumina platform from 96-array format to 12-array format with no apparent batch differences present. For the tissue-differential analysis results were considered to be replicating if the fixed effect of interest (β) had a p-value<0.05 and consistent direction of the effect.
