Figure 5

Concordances of different microarrays in terms of percentage of overlapping genes (POG) The x-axis represents the number of genes (2L) selected as differentially expressed, and the y-axis represents the overlap (%) of two gene lists selected from the two experiments under comparison. All of the genes in the two compared experiments were first filtered with a p < 0.05 cutoff and then ranked by fold changes in up- and down directions. Next, the top L genes with the largest fold changes were selected as differentially expressed from each direction and the DEG list containing 2L genes from each experiment was used for cross-experiment comparisons. L was increased from one to the lower number of genes in both regulation directions with a step of one. The red crosses represent the reference line, i.e., the mean POG of DEG lists in four comparisons of microarray reference data groups in MAQC project: ABI, AG1, ILM, and GEH versus AFX. The dashed and dotted green and blue markers showed the lower limit and the upper limit of the 95% confidence intervals, respectively, for the reference line.