Figure 1

Comparisons of probe level patterns across replicates and treatments for selected genes. Each line color (in Panels A, B, and C) represents a probe level pattern on a specific array. Blue and black lines show probe level patterns on arrays from time = 0. Red and orange lines show probe level patterns on arrays for time = 96 hours. The first row shows probe level patterns for the highest up-regulated gene by fold change (Hspb1). The second row is a randomly selected gene. The third row is the most down-regulated gene by fold change. The x-axis for each plot in (Panels A, B, and C) is probe number (1 through 11). (Panel A) shows log₂ of raw probe intensities by probe number. (Panel B) shows log₂ array-centered intensities by probe number. The log₂ quantile normalized mas-background-corrected probe intensities are shown in (Panel C). (Panel D) shows summary gene expression estimates using median polish. The summarization method used is exactly like the RMA method except that mas-background correction is used instead of rma background correction.