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  (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.
Rubin BMC Bioinformatics 2009 10:292 doi:10.1186/1471-2105-10-292