Quantitative PCR of significantly differentially expressed genes show better agreement with arrays than sequencing. 192 randomly sampled significantly differently expressed genes were analyzed by qPCR. qPCR results are highly correlated with both microarrays (R = 0.86, bootstrap 95% CI: 0.7043 – 0.953) (A) and sequencing results (R = .82, bootstrap 95% CI: 0.7031 – 0.8917) (B). However, the subset of the tested genes that were called significantly differentially expressed by the arrays only (see Fig. 1A, red dots) were more highly correlated (R = 0.925, bootstrap 95% CI: 0.8621 – 0.9648) (C) than the subset of genes that were called significant by sequencing (see Fig. 1A, green) (R = 0.518, bootstrap 95% CI: 0.3227 – 0.7069) (D). Error bars represent 95% confidence intervals for the differential expression measurements.
Bloom et al. BMC Genomics 2009 10:221 doi:10.1186/1471-2164-10-221