Fig 3. Correlation estimates show widely varying performance on simulated data.

(N = 5000 “genes”) against the known true correlations used to generate the data (dotted line). 50 replicates were performed at each parameter value. A, Varying true correlation from 0.1 to 1.0 with a fixed reliability (ratio of true to total variance) of 0.7. B, Varying reliability from 0.1 to 1.0 with a fixed true correlation of 0.9. C, Varying the number of genes with detected gene products from 100 (2%) to 5000 (100%) with a fixed reliability of 0.7 and fixed correlation of 0.9, with gene data missing at random. D, As in C, but with gene data missing non-randomly according to the sigmoidal model described in Methods, such that low-expression gene products are less likely to be detected.