Figure 3

Selection of the global rank-invariant set size. A. The effect of selecting different sized Global Rank-invariant Sets (GRiS) on the calibration curves for a given sample. Each curve shows the GRSN calculated adjustment value as a function of expression value (for a given sample). Red curves are from GRiS sizes of 100, 200, 300, 400, and 500. Green curves are from GRiS sizes of 2000, 4000, 6000, 8000, and 10000. The blue curve is from the default GRiS size of 5000. GB dataset comparing Fanconi vs. Normal using MAS 5.0 processed data on left and RMA processed data on the right (notice different y-axis scales). B. The effect of changing the GRiS size on the selection of significantly regulated genes. Each bar represents the difference in the lists of significant genes found due to a change in the size of the GRiS. The red bar represents the default size of 5000 vs. none (not using GRSN) and is meant to show the magnitude of the effect of applying GRSN (a reference point for the other bars). The three blue bars represent, in order from left to right, the difference of 5000 to 10000, 10000 to 15000, and 15000 to 20000. Top Row – GB dataset comparing Fanconi vs. Normal using MAS 5.0 processed data on left and RMA processed data on the right. On left, GSE6802 dataset comparing R vs. C, using RMA. On right, 339RS dataset comparing TA vs. C using RMA.