Figure 1
Overview of the eCADS model. The left panel summarizes the model of equation 2. The observed fluorescence intensity (y R or y G ) for agene with x RNA is modeled as the sum of the average dye function d, the function corresponding to the dye used for labeling (δ R or δ G ), and an array-specific function a. Since we do not know the true RNA amounts x, we warp the x-axis so that every x value is replaced with d(x); these 'warped RNA amounts' are essentially group means adjusted gene-by-gene for bias (see Model formulation). The curves in the right panel are analogously warped versions of the curves in the left panel, now representing deviations from the group mean (the straight line). The warping enables the estimation of the model without affecting the relationships of interest.