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Table 4 Comparison between the GPA and housekeeping gene normalizations based on simulated boutique array data with the Balagurunathan's method. The data sets are simulated without or with dye bias and include 1000 genes in 10 slides with 60% differentially expressed genes. 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

Ratio(1) Method Without dye bias With dye bias
   ν (2) β (2) ν β
5:5 Raw 0.1147 0.008632 0.1144 0.007297
  Housekeeping gene 0.1133 0.008569 0.1164 0.007326
  GPA 0.03285 0.002833 0.03349 0.002584
7:3 Raw 0.1139 0.007859 0.1186 0.007902
  Housekeeping gene 0.1157 0.007937 0.1195 0.007427
  GPA 0.0288 0.00315 0.03133 0.003334
9:1 Raw 0.1172 0.007659 0.1178 0.007916
  Housekeeping gene 0.1187 0.006898 0.1152 0.009463
  GPA 0.02785 0.004814 0.02802 0.005119
  1. (1) Ratio of up- to down-regulated genes
  2. (2) ν and β : the median of variance and bias, respectively, of MSE