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New statistical algorithms for Monitoring Gene Expression on GeneChip® Probe Arrays

illustrates the linearity of dose response from the 14 spiked transcripts and the upper and lower confidence limits. It also demonstrates that signal calculation in the statistical algorithms (MAS 5.0) generates signal values that accurately reflect the true concentration.

As with Figure 2, no signal value in Figure 4 is ever negative or zero. This allows signal values to be easily transformed to a logarithmic scale.

The effects of altering tunable confidence parameters on Present calls were studied in a yeast Latin Square experiment. The tunable parameter controlling the number of Present calls is termed a1 (alpha1). Altering a1 results in a shift in the p-value cutoff used to make a Present call.

This parameter was varied in this analysis to determine the effect on the number of Present calls at different concentrations.

Calls at higher concentrations are typically unaffected by altering a1. At concentrations below 8 pM in this experiment, a decrease in stringency (i.e., increase in a1 from 0.04 to 0.1) results in an increasing number of Present calls. As Figure 5 shows, a1 may be varied to obtain sensitivities using MAS 5.0 that are greater or lower than those obtained with MAS 4.0. However, an increase in a1 produces a corresponding increase in the number of false positive calls, as seen at the 0 pM concentration. It should be noted that false positives can easily be flagged by their high p-values.

Comparison Calls Generated by MAS 4.0 and MAS 5.0 Show Concordance

Analyses were performed to study the concordance between comparison calls generated by MAS 4.0 and MAS 5.0. To assess “No Change” calls, comparison analysis was performed on replicate Human Genome U95A arrays from the human Latin Square experiment, where transcript group concentrations were identical between experiments. Therefore, a No Change call is expected for each transcript group
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