Data was imported into R using the beadarray package [54]. Data was background corrected by subtracting the background intensity from the foreground levels and bead summary data was calculated using the Illumina method. Data were thereafter quantile normalised between arrays, log2 transformed and expression intensities were extracted. Normalisation was done separately for abdominal and gluteal adipose tissue samples for miRNA eQTL analysis, while in the case of tissue-differential expression analysis, all data were normalised together. Probes were excluded from further analysis if the 75th percentile of expression level in either tissue was lower than the 25th percentile of array control probes, resulting in 1131 (out of 1146) probes included for further analysis. Outliers were detected using Principal Component Analysis (PCA) and the Hotelling T2 test on the first 3 PCA score components; outliers were defined as being outside the 0.99 confidence interval in the score space. One array was defined as an outlier by PCA, two additional arrays were considered as outliers due to substantially higher overall background and foreground signals than other arrays, in total three arrays were excluded
