Figure 21

Comparison with other methods. (a) Comparison of mac1 candidates for differentially-expressed genes defined using adjusted supsmu-based STIs and by Hughes et al. [18]. Red and blue dots denote genes designated as being up-regulated and down-regulated, respectively, by the Hughes et al. 'gene-specific' error model at p-value ≤ 0.05. The 95%, 99%, 99.8%, 99.98% and 99.998% adjusted supsmu-based STIs are shown (covered with probability at least 0.9999). The vertical dotted line marks the location of the minima of the empirical hyperbolas. (b) Comparison 95% adjusted supsmu-based STIs (red) with statistical intervals based on three other single-slide methods: a hierarchical Gamma-Gamma-Bernoulli model [19] with the posterior odds of change in expression 1:1(innermost), 1:10 (middle) and 1:100 (outmost); mixture of orthogonal residuals with posterior probability of differential expression 95% (blue) based on approach from Sapir and Churchill [20]; and 95% band using asymmetric density function for raw ratios (Cy5/Cy3) assuming the same coefficient of variation for both fluors [17].