BMC Genomics 2008, 9:230 http://www.biomedcentral.com/1471-2164/9/230 BFoigxuprloet1of LR values for different spot classes Boxplot of LR values for different spot classes. The limits of the central box represent the 1st and 3rd quartile. The line in the middle of the box marks the median. The lines in the ends of vertical broken lines represent minimum and maximum LR values observed. The stars along the broken lines indicate the 5th and 95th percentiles. rithm of the expected values of Table 1. Hybridizations with T control for spot sets with an expected LR greater than 0 appear to produce LR distributions with a median more distant from 0 but with higher amplitude (Panels A and B) as compared with the same sets in the mix control experiments (Panels C and D). In the hybridizations with a mix control, for the spot sets that are expected to gener- ate a positive LR, the dispersion is reduced as compared with the spot sets in which the test is absent (Panels C and D). In the former distributions, both test and control have signals above noise levels, while for the latter the signal of the test is just random noise, contributing to a higher LR variability. These random noise signals are also the reason for higher dispersion in LR distributions for hybridiza- tions with the T control in spots where either the test or the control is not specifically recognized by the spots. Threshold independent analysis To evaluate the discriminatory power of LR distributions without having to specify an exact threshold value, we compared de AUC of ROC plots for the hybridizations with different controls, analyzing either all spots together or divided into two mutually exclusive classes. The AUC values have a useful quantitative meaning: if one takes two spots, one with a true present call and another with a true absent call, the AUC is the probability that the LR value of the first spot is higher than that of the second spot [23]. Analyzing all spots together (Figure 2, panel A) we detected a significant increase in AUC if the mix control is used (p = 0.008). Carrying out two separate analyses according to spot class (Figure 2, panel B), we obtain a higher discriminatory power for spots recognizing T genes, when using a T control. In hybridizations with mix Page 4 of 11 (page number not for citation purposes)