Inter-site reproducibility of log2 FC and log2 t-statistic. a: log2 FC of site 1 versus log2 FC of site 2; b: log2 t-statistic of test site 1 versus log2 t-statistic of test site 2; and c: log2 FC of test site 1 versus log2 t-statistic of test site 1. Shown here are results for comparing sample B and sample A for all "12,091" genes commonly probed by the five microarray platforms. The inter-site reproducibility of log2 FC (a) is much higher than that of log2 t-statistic (b). The relationship between log2 FC and log2 t-statistic from the same test site is non-linear and the correlation appears to be low (c).
Shi et al. BMC Bioinformatics 2008 9(Suppl 9):S10 doi:10.1186/1471-2105-9-S9-S10