Figure 7

GRSN impacts gene discovery. Averaged fold change M vs. A plots as in Figure 5B, but with color coding added to show genes passing fold change and statistical thresholds for significant differential regulation between experimental conditions. Statistical thresholds reported in this figure are for FDR adjusted p-values from standard t-tests. A) GB data comparing 14 Fanconi Anemia samples to 11 Normal samples and plotted using values from RMA method alone (left panel) and using values from RMA with GRSN (right panel). Both plots are color coded to show genes found to be significantly changed (FC of at least 1.5 and FDR of no more than 0.05): genes found only when using RMA alone are in blue, genes found only when using RMA with GRSN are in red, and genes found in both cases are in yellow. The horizontal colored lines show the fold change cutoff applied to the respective summary and normalization methods. B-C) Color coding is modified so that blue genes are shown only in the left panel and red genes are shown only in the right panel. B) GSE6475 data comparing 6 AL (acne lesion) replicates to 6 AN (acne normal) replicates. Samples are plotted as in A. C) SS data comparing 6 mutant samples to 6 wild type (3 male and 3 female for each condition). No FC threshold is applied in this example and the FDR threshold is set to 0.10. D) GSE7664 data comparing 8 bt (treated) to 8 med (untreated) samples plotted as in A.