Bubble plots from the simulation example. Bubble area is proportional to weights used in the meta-analysis. Dashed lines represent the 95 percent confidence interval for the true value of the SLR, adjusted to control the FDR for all 1322 genes at 0.05. The red dotted line represents the true SLR value. The green bubbles represent labs which claimed significant differential expression for the gene. When zero lies outside the confidence interval, the meta-analysis declares the gene significantly differentially expressed. (a) SLR estimates from the six labs for a particular gene, with fixed effects weights. (b) Plot for the same gene as in (a), but with random effects weights. (c) Plot for one of the twenty-one Integration-Driven Discovery (IDD) genes declared significant by none of the six simulated labs but significant by the random effects meta-analysis. (d) Plot for one of the four Integration-Driven Revision (IDR) genes declared significant by multiple labs but not significant by the random effects meta-analysis.