Figure 13.

Plots of within-chip log amplitude z-scores for two HG-U133A Spike-in Experiment "Unanticipated Positives". These two genes, 204890_s_at (shown on the left) and 204891_s_at (on the right) are neither in the original list of spiked-in genes for the Affymetrix HGU-133A Latin Square experiment, nor in the expanded list created by McGee and Chen [5] (although they considered including them but chose not to). However, as shown in this comparison of experimental conditions 14 (replicates in red) and 1 (replicates in cyan) of the Latin Square design, these genes are obvious candidates for a category we call "unanticipated positives". It is very difficult to image that these profiles could have come from probe sets with identical probe-level distributions for the experimental conditions 1 and 14.