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 |