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Table 3 Parameter estimates for the total data set consisting of 10759 genes and for the "conservative set" of 2721 genes.

From: Effects of mRNA amplification on gene expression ratios in cDNA experiments estimated by analysis of variance

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
σ A (array) Random 0.28 0.30
σ B (batch) Random 0.041 0.041
σ C (gene) Random 1.36 0.98
σ AD Random 0.039 0.040
σ GP Random 0.85 0.79
σ CG Random 0.74 0.54
σ AG Random 0.44 0.44
σ DG Random 0.048 0.050
σ CGP Random 0.22 0.028
σε Random 0.22 0.22
  1. 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. σ CGP is the cell line specific GP effect and is the effect of primary interest.