2.3.2. Agilent Human miRNA Microarray (V1)
Images were scanned using the Agilent Feature Extraction (AFE) software (version 11.0.1.1), obtaining the total gene signal (TGS) for all miRNAs on the array. Negative values were transformed by adding, for each array separately, the absolute value of the minimum TGS intensity on the array as extracted by the AFE + 2 before log2 transformation [20]. Data extracted from AFE were imported in the R environment [21] and processed using the AgimiRNA package, available in Bioconductor [22,23].