Figure 1.

Concordance for inter-site comparisons. Each panel represents the POG results for a commercial platform of inter-site consistency in terms of DEGs between samples B and A. For each of the six gene selection methods, there are three possible inter-site comparisons: S1–S2, S1–S3, and S2–S3 (S = Site). Therefore, each panel consists of 18 POG lines that are colored based on gene ranking/selection method. Results shown here are based on the entire set of "12,091" genes commonly mapped across the microarray platforms without noise (absent call) filtering. POG results are improved when the analyses are performed using the subset of genes that are commonly detectable by the two test sites, as shown in Figure 2. 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 test sites at a given number of DEGs.

Shi et al. BMC Bioinformatics 2008 9(Suppl 9):S10   doi:10.1186/1471-2105-9-S9-S10