Figure 1

An example of a standardized probe set plot, with probe-by-probe ANOVA results and summaries. The left portion of this chart contains the probe set plot for the gene 205398_s_at from the HG-U133A Latin Square experiment for a large change in spike-in concentrations. Replicates are shown in cyan for 512 pM concentrations and in red for 256 pM. The table on the right lists the p-values for the ANOVAs performed at each probe position. "Total p" is the product of the probe-level ANOVA p's, and Per-probe p is the nth root of Total p, where n is the number of probes in the probe set. For this gene, rankings (among all genes on the six chips and two concentrations involved in the comparison) based the median of the (1-p)'s and on the trimmed Total p (i.e., the product of all but the highest and lowest of the probe-level p's) are comparable and consistent with the experimental design. The (unadjusted) P-value of the median was obtained directly from a beta distribution parameterized by the number of probes in a probe set.