Figure 2

Single-gene significance and agreement with operons. For each data set and for three methods of assessing significance (OpWise, OpWise without bias, and significance analysis of microarrays), we divided the changers into eight groups of genes with different levels of confidence. The x axis shows the average confidence within each group of genes. For each group, the y axis shows the adjusted agreement with operon pairs (the adjusted proportion of pairs which have the same sign of log-ratio), which ranges from 0 for random data to 1 for perfect measurements. We also show average results from simulations for each data set (simulated and analyzed with the OpWise model). The error bars give the 95% confidence interval (from a t test) for the mean agreement for each group from the OpWise significance values. The odd left side of the ecox SAM curve is due to noise in the local FDR.