Figure 3  Description of the REAP Algorithm Comparing Exon Array Signal Estimates from hCNS-SCns and Cyt-ES
(A) Histogram of Pearson correlation coefficients computed from median signal estimates for probesets between Cyt-ES versus hCNS-SCns for genes (blue bars). Genes were required to have more than five probesets localized within the exons in the gene. Red bars represented Pearson correlation coefficients computed from exons with shuffled signal estimates.
(B) Each probeset contained probeset-level estimates from three replicates each, (a, b, c) in Cyt-ES and (d, e, f) in hCNS-SCns. The five points summarizing the log2 probeset-level estimates are indicated by black filled circles.
(C) Each probeset was summarized by five points. Scatter plots of signal estimates for probesets that were present in at least one cell type (Cyt-ES or hCNS-SCns) for the EHBP1 gene. Probesets were considered present if the DABG p-value was <0.05 for all three replicates in the cell type. A regression line derived from robust linear regression with MM estimation is indicated. Points above the line represent probesets within exons that were enriched in Cyt-ES and points below represent exons that were enriched in hCNS-SCns. Points close to the regression line are not significantly different in Cyt-ES versus hCNS-SCns. Boxed points represented the five-point summary of a probeset that was significantly enriched in Cyt-ES but was skipped in hCNS-SCns.
(D) Histogram of studentized residuals for points from the scatter plot in (C) in EHBP1.
(E) The histogram of studentized residuals for all points for all analyzed probesets (100 bins).
(F) The scatter plot of studentized residuals generated from comparing Cyt-ES versus hCNS-SCns and hCNS-SCns versus Cyt-ES of 5,000 randomly chosen probesets.