Figure 2

RMA decomposition of probe-level Affymetrix data. Panel A shows the background-adjusted and normalized probe-level data for PRRX1, from the Affymetrix mixture dataset (see Methods). The probes are displayed in the order which they map to the human genome (not to scale), and lines join all probe intensities of the same sample. PRRX1 is expressed significantly higher in heart tissue compared to brain. Three replicates of pure heart tissue are shown as red lines; green lines represent pure brain tissue replicates and the blue lines represent a mixture of 75% brain tissue and 25% heart tissue. Panel B shows the estimated relative probe effects. Panel C shows the chip effects (i.e. summarized expression levels) and Panel D shows residuals, using the same colour scheme.