Expression values were calculated following the pre-processing procedure: 1) GCRMA background correction, 2) log2 transformation, 3) quantile normalization, and 4) median-polish probeset summarization using Partek Genomics Suite v6.23 (PGS; Partek Inc., St. Louis, MO) [91, 92]. The batch effect removal option in PGS was used to control for batch effect. mRNA and miRNA microarray quality was assessed by principal component analysis (PCA) of the expression values for both the miRNA and mRNA arrays. Samples were plotted along the first three principle components (PCs) to identify potential microarray outliers. Of the 36 HG-U133A 2.0 microarrays, one AD sample did not load onto two of the first three PCs and was removed from subsequent analysis (n = 35). No samples were removed from miRNA microarray analysis.
