Bubble plots from the EAE 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 green bubbles represent experiments 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) Bubble plot for one of the sixty-five Integration-Driven Discovery (IDD) genes declared significant by none of the seven observed experiments but significant by the random effects meta-analysis. (b) Bubble plot for one of the thirty-two Integration-Driven Revision (IDR) genes declared significant by all seven observed experiments but not significant by the random effects meta-analysis.