Pre-processing steps. AgiMicroRna includes two distinct pre-processing protocols for transforming the raw probe level data into the processed data that contain the summarized and normalized microRNA gene signals. The first protocol comprises the following steps: 1) acquisition of the TGS processed by AFE, and 2) normalization between arrays by scale or quantile methods. The second option uses the RMA algorithm via the following steps: 1) the raw mean signal can be background corrected (optional, see recommendations in the text); 2) the signal is normalized between arrays by quantile normalization, and 3) the probe level data is summarized into a single microRNA measure. Selected microRNAs can be filtered out according to the Flags assigned to each probe by the Agilent Extraction Software.