Concordance between FC and P based gene ranking methods ("12,091 genes"; test site 1). Each POG line represents a platform using data from its first test site. The x-axis represents the number of selected DEGs, and the y-axis is the percentage (%) of genes common in the DEGs derived from FC- and P-ranking. Shown here are results for comparing sample B and sample A for all "12,091" genes commonly probed. When a smaller number of genes (up to a few hundreds or thousands) are selected, POG for cross selection method comparison (FC vs. P) is low. For example, there are only about 50% genes in common for the top 500 genes selected by FC and P separately, indicating that FC and P rank order DEGs dramatically differently. When the number of selected DEGs increases, the overlap between the two methods increases, and eventually approach to 100% in common, as expected. The low concordance between FC- and P-based gene ranking methods is not unexpected considering their different definitions and low correlation (Figure 7c).
Shi et al. BMC Bioinformatics 2008 9(Suppl 9):S10 doi:10.1186/1471-2105-9-S9-S10