Alternative Probes Sets. (A) Z-values of heat shock, pre-heat shock and ratio probes. Most outliers were identified at the high end of each probe set. (B) Comparison of an alternative probe set (BCAL0317) with repeatable signal intensity and heat shock/pre-heat shock ratios. Ratio levels all return the same conclusion of no change in expression. (C) No probes were identified as signal intensity outliers in the set for BCAL1925, however both probes 2 and 4 contribute different probe conclusions (decrease in gene expression) than the majority of this set (no change in gene expression). (D) Conversely, in the set of alternative probes designed from BCAL1467 probe 4 is identified as an outlier, but error in signal intensity does not lead to incorrect up/down call.