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Table 3 ANOVA analysis before and after normalization

From: Normalization of low-density microarray using external spike-in controls: analysis of macrophage cell lines expression profile

  Before normalization After normalization
Source of variationa) sum of squares degree of freedom p-value % of variance sum of squares degree of freedom p-value % of variance
Spike concentrationb) 169.084 3 0.000 48.3% 0.762 3 0.000 1.0%
Spike characteristicsc) 62.295 7 0.000 17.8% 50.094 7 0.000 40.4%
Array positiond) 1.530 11 0.000 0.4% 1.247 11 0.000 0.6%
Concentration* characteristicse) 104.040 21 0.000 29.7% 58.848 21 0.000 47.4%
Errorf) 13.477 1240   3.8% 13.105 1240   10.6%
Totalg) 332.992 1282    119.280 1282   
  R Squaredh) = 0.958 R Squaredh) = 0.887
  1. a) The variability is subdivided into independent variances. b) Amount of spikes in the experiment. c) Base composition, length of the mRNA and interaction with other RNA molecules. d) Spot size, tips, slide homogeneity, printer accuracy. e) Interaction between spike concentration and spike characteristics. f) Residual variability. g) Corrected total variability. h) R squared calculated from linearity test resulting from the amount of variance in the dependent variable that is accounted for by the corrected model.