Effect of middle base pair and probe number at gross array level. The top left diagram (A) shows box plots by probe number (1–11) for all transcripts in array C. A slightly increasing trend can be seen. The top right diagram (B) shows box plots of probes in array C by middle base pair (A, C, G, and T) of the probe. The comparative levels are consistent with that described in the Naef and Magnasco  paper. The diagrams on the second row (C and D) show box plots of log2 probe intensities categorized by both probe number and middle base pair for all probes in array 3. The slight increasing trend at the array level is too weak to pick up in the plots of individual probe sets (Figure 1).