Figure 2

Plot showing RPKM values of 186 differentially expressed transcripts and their absolute expression (measured as copies/cell). Log10 RPKM values for controls and cases are shown on the x and y-axes, respectively. The dashed diagonal line represents equal RPKM values for both cases and controls, and hence no differential expression. Thus, the orthogonal distance to the dashed line of a point indicates the amount of differential expression. The blue numbers on the dashed line indicate the log10 measure of copies/cell for the seven spike-in RNA controls (ranging from 1–100000), and the position along the x and y-axes indicate the corresponding RPKM values recorded for these spikes. Based on a linear regression model for copies/cell as a function of RPKM, predictions for absolute expression measured as copies/cell for the 186 transcripts were made from these spike-in values. For each position, the average of the RPKMs corresponding to the x and y-coordinate values yield predictions of cell copies based on this model and a corresponding color shown in the background of the plot ranging from green (low) to red (high).