Inter-site concordance based on FC, t-test, Wilcoxon rank-sum test, and SAM. Affymetrix data on samples A and B from site 1 and site 2 for the "12,091" commonly mapped genes were used. No flagged ("Absent") genes were excluded in the analysis. For the Wilcoxon rank-sum tests, there were many ties, i.e., many genes exhibited the same level of statistical significance because of the small sample sizes (five replicates for each group). The tied genes from each test site were broken (ranked) by random ordering. Concordance between genes selected completely by random choice is shown in red and reaches 50% when all candidate genes are declared as differentially expressed; the other 50% genes are in opposite regulation directions. SAM improves inter-site reproducibility compared to t-test, and approaches, but does not exceed that of fold-change.
Shi et al. BMC Bioinformatics 2008 9(Suppl 9):S10 doi:10.1186/1471-2105-9-S9-S10