Table 3.
Parameter estimates for the total data set consisting of 10759 genes and for the "conservative set" of 2721 genes.
| Parameter | Type of effect1 | Estimate Total set | Estimate Conserved set |
| μ | Fixed | 10.56 | 12.18 |
| C (cell line 2; U2OS) | Fixed | 0.086 | -0.028 |
| D (Cy3) | Fixed | -0.026 | -0.022 |
| P (non-amplified) | Fixed | -0.74 | -1.14 |
| CP22 (cell line 2 and non-amplified) | Fixed | -0.0043 | 0.0089 |
| σA (array) | Random | 0.28 | 0.30 |
| σB (batch) | Random | 0.041 | 0.041 |
| σC (gene) | Random | 1.36 | 0.98 |
| σAD | Random | 0.039 | 0.040 |
| σGP | Random | 0.85 | 0.79 |
| σCG | Random | 0.74 | 0.54 |
| σAG | Random | 0.44 | 0.44 |
| σDG | Random | 0.048 | 0.050 |
| σCGP | Random | 0.22 | 0.028 |
| σε | Random | 0.22 | 0.22 |
Annotations: μ = overall mean signal intensity, C = cell line type, D = labeled dye, P = protocol. 1 Of the fixed effects, C, D, and P have two levels while CP is an interaction between two fixed effects. The random effects were modeled as independently normally distributed random effects with zero mean and constant standard deviation. σCGP is the cell line specific GP effect and is the effect of primary interest.