Comparison of SAGE and Affymetrix HG-U133A GeneChips results using the scaled ratios between Wilms' tumor and Stratagene Universal Reference RNA expression levels. A: Up/Down classification. The red points in the upper-right and lower-left were considered to be in agreement between the platforms. B: contingency table diagonal based on the classification of gene expression ratios into log (10-fold) classes. The genes falling in the classes on the diagonal were considered to be in agreement between the platforms. C: Pearson correlation coefficient. The correlation coefficient was 0.472 and corresponds to a linear regression line with a slope of 0.492 (solid line) The Y = X line with a slope of 1 (dashed line) is the expected line when both platforms have identical expression patterns. D: absolute between-platform ratio differences (see Figure 4) were calculated and classified: 0–0.5 (red), 0.5–1.0 (green), 1.0–1.5 (blue), 1.5–2.0 (magenta), 2.0–2.5 (light blue). These classes represent an approximate less then 3, 10, 30, 100, and 300-fold difference, respectively, between the two platforms. The points in the 0.5 zone were considered to be in agreement between the platforms.
van Ruissen et al. BMC Genomics 2005 6:91 doi:10.1186/1471-2164-6-91