Concordance for cross-platform comparisons. Panel a: Based on the data set of "12,091" genes (without noise filtering); Panel b: Based on subsets of genes commonly detected ("Present") by two platforms. For each platform, the data from test site1 are used for cross-platform comparison. Each POG line corresponds to comparison of the DEGs from two microarray platforms using one of the six gene selection methods. There are ten platform-platform comparison pairs, resulting in 60 POG lines for each panel. The x-axis represents the number of selected DEGs, and the y-axis is the percentage (%) of genes common to the two gene lists derived from two platforms at a given number of DEGs. POG lines circled by the blue oval are from FC based gene selection methods with or without a P cutoff, whereas POG lines circled by the teal oval are from P based gene selection methods with or without an FC cutoff. Shown here are results for comparing sample B and sample A.
Shi et al. BMC Bioinformatics 2008 9(Suppl 9):S10 doi:10.1186/1471-2105-9-S9-S10