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

compared, the results are highly similar, with a regression ratio of 0.94. Similar results were obtained across multiple tissues and with replicates (data not shown). This similarity was also observed on arrays representing different organisms. The regression ratios for these comparisons were in the 0.92-0.93 range for M. musculus, A. thaliana and S. cerevisiae , and 0.96-0.97 for D. melanogaster and E. coli .

The occurrence of negative values in MAS 4.0, seen in the two left quadrants in Figure 2B, has been eliminated from MAS 5.0. The corresponding output in MAS 5.0, termed “Signal” has no negative and zero values as is evident in the lower two quadrants of Figure 2B.

Added Statistical Quality Measures and Tunable Parameters

An added benefit of the statistical algorithms in MAS 5.0 is the inclusion of probability values (statistical significance) associated with detection and comparison calls. This additional metric allows users to assess the significance of results, and if desired, adjust the balance between sensitivity and specificity. For example, higher confidence in expression calls (greater specificity) can be achieved by accepting fewer Present calls (lower sensitivity). Conversely, greater sensitivity may be achieved at the expense of lower specificity. The inverse relationship between sensitivity and specificity in MAS 5.0 was examined by monitoring detection calls in the set of experiments described below. As shown in Figure 3, a greater number of accurate Present calls is made by MAS 5.0 at concentrations below 4 pM using the default p-value setting. However, the small number of false positives is also slightly greater for MAS 5.0 in this experiment, as seen at the 0 pM concentration. The sensitivity and specificity may be varied in a predictable fashion by varying the default setting for p-value cutoff.

Figure 4
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