Results of ANOVA for the Mus Musculus Plat gene. In panels B-E of this figure the color of the plotted data points represents the fluorochrome that was used to label the sample (green = Alexa 546, Red = Alexa 647). A Graphical display of the Variety term estimate and standard error for the relative Plat gene expression for mice WT2, WT3, KO1, KO2, KO3 referenced to WT1 (the a in front of WT1, WT2 and WT3 is simply a label marker). Solid lines represent the final estimates after removal of outliers, while the dashed lines represent estimates before removal of outliers. The Dye2 (Alexa 647) effect and its standard error are also shown. B, C Transformed and normalized intensities plotted by sample (B) or hybridization (C). Colored circles (confident) and triangles (below user defined confidence threshold) represent the normalized measured intensities for each element (i.e. spot), and dashes represent the calculated intensities from the ANOVA model. An x denotes a point that was identified as an outlier. D A normal Q-Q plot for all data providing an indicator of the normality of the residuals. E The Cook's distance plot illustrating the influence of each data point on the fit of the model.