The Single-Channel Array Normalization (SCAN) pre-processing procedure [40], implemented in the SCAN.UPC package (version 2.24.1) from Bioconductor [41, 42], was applied on all microarray data sets for probe correction, normalization and removal of array-specific background noise. SCAN is a single-sample normalization method that adjusts for array type. Therefore, SCAN is particularly suited for integrative analyses of microarray data derived from different Affymetrix array platforms [40].
Quality control of all raw and pre-processed microarray data was conducted using the arrayQualityMetrics package (version 3.38.0) [43] from Bioconductor.
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