The miRNA from the Nanostring RCC files were re-annotated to match the definitions from the miRBase v19. The raw data from the Nanostring RCC files were accumulated and the probe-specific backgrounds were adjusted according to the Nanostring guidelines with the corrections provided with the probe sets. After correcting for the probe-specific backgrounds, a three-step filtering of miRNA and sample expressions was performed. First, miRNA that had less than 95% of samples with an expression level were removed. This is followed by removing samples that had less than 95% of miRNAs with expression measures. Thus, the call-rates for the samples and the miRNA are set at 95%. Finally, all miRNA whose absolute value is less than 15 in at least 50% of the samples were removed to eliminate miRNA that had negligible expression in brain samples. After the miRNA and sample filtering, the dataset consisted of 309 miRNAs and 702 subjects. A combination of quantile normalization and Combat33, specifying the cartridges as batches for the miRNA data, was used to normalize the data sets.
