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Table 5 Comparison between the GPA and housekeeping gene normalizations based on simulated boutique array data with the SIMAGE method. The data sets include 1000 genes in 50 slides with 60% differentially expressed genes and the ratios of up-regulated to down-regulated genes are 5:5, 7:3, and 9:1, respectively.

From: Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data

Method 5:5(1) 7:3(1) 9:1(1)
  ν (2) β (2) ν β ν β
Raw 1.467 0.4234 1.178 0.4687 1.532 0.8552
Housekeeping gene 0.2055 0.4642 0.1842 0.478 0.176 0.9346
GPA 0.111 0.3402 0.1059 0.3296 0.1194 0.5331
  1. (1) Ratio of up-regulated to down-regulated genes
  2. (2) ν and β: the median of variance and bias, respectively, of MSE