Figure 2

An example of why the median of the (1-p)'s might be a better measure of differential expression than the (trimmed) Total-p. This chart contains the probe set plot and ANOVA results for the gene 208010_s_at from the HGU-133A Latin Square experiment for concentrations of 128 pM (replicates in cyan) and 64 pM (replicates in red). The lack of a significant difference between conditions at probe positions 1,2, 6 and 7 adversely affects even the trimmed Total-p, while the median-based ranking of this gene (among all 22300 genes on the two chips involved in the comparison) is much more consistent with the Latin Square design. This is one among many cases for which the median seems to be the most robust measure.