Figure 6
From: Platform dependence of inference on gene-wise and gene-set involvement in human lung development
Associations between p-value rankings and significance groups and correlation. A) Two-dimensional density plot of correlation versus p-value ranking (Illumina and Affymetrix) for different significance groups. B, C) Genes in Gai and Gns have the lowest and highest p-value rankings for both Affymetrix and Illumina while those in Gi and Ga have intermediate rankings. The mean Illumina ranks for Gai, Gi, Ga, and Gns are 306, 385, 6277, and 8469, respectively. The mean Affymetrix ranks for Gai, Ga, Gi, and Gns are 915, 1993, 7763, and 9537, respectively. Using the Wilcoxon rank sum test, the Illumina p-value ranking for Gai is significantly different from Gi and Ga (p = 1.517 × 10-5 < 2.2 × 10-6). Similarly, the Illumina p-value ranking for Gns is significantly different from Gi and Ga (p < 2.2 × 10-16 for both). The Affymetrix p-value ranking for Gai is significantly different from Gi and Ga (p < 2.2 × 10-16 for both). Similarly, the Affymetrix p-value ranking for Gns is significantly different from Gi and Ga (p = 2.338 × 10-9 and < 2.2 × 10-16).