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Table 1 Comparison among different normalization methods based on simulated normal microarray data with the Balagurunathan's method. The data sets are simulated without or with dye bias and include 1000 genes in 10 slides with 5% differentially expressed genes. The ratio of up-regulated to down-regulated genes is 1:1. The additional file 3 contains the full data sets.

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

Method Without dye bias With dye bias
  ν (1) β (1) ν β
Raw 0.1182 0.004627 0.1231 0.004586
Global 0.1179 0.004732 0.1223 0.00473
Lowess 0.1143 0.005368 0.1182 0.004976
Scale 0.1113 0.004666 0.1201 0.004515
Quantile 0.1149 0.005226 0.1212 0.004716
VSN 0.06294 0.002581 0.06314 0.002541
GPA 0.02122 0.00117 0.02069 0.00119
Global+Scale 0.1117 0.004579 0.1191 0.004595
Global+Quantile 0.1149 0.005226 0.1212 0.004716
Global+GPA 0.02122 0.001174 0.02068 0.001156
Lowess+Scale 0.1088 0.005161 0.1153 0.005067
Lowess+Quantile 0.1133 0.005085 0.1198 0.004812
Lowess+GPA 0.02215 0.001279 0.02205 0.00134
  1. (1) ν and β : the median of variance and bias, respectively, of MSE.