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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