Figure 8

Smoothed estimates of the average rank of expression values and squared deviations (with respect to the appropriate group mean) of the three control replicates for the (a, b) original and (c, d) re-loessed datasets. The x-axes correspond to the rankit of the log of the product of the expression means. The y-axes correspond to the observed ranks and were calculated across all six samples. If the control (C) and spike-in (S) expression values are interchangeable, the average rank of the control values should be 3.5. (c) Re-loessing adequately re-centers the control expression values relative to the spike-in expression values. (d) Despite re-loessing, however, the ranks of the squared deviations for the control replicates remain below those of the spiked-in replicates, suggesting that the expression values for the control replicates are less variable than those for the spiked-in replicates. This difference appears to be intensity dependent. Used with permission from [15].