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Microarray Suite 5.0 uses two independent sets of algorithms to generate results from GeneChip expression arrays. One set of quantitative algorithms compute Signal and Signal Log Ratio directly from the hybridization intensities of probes. The other set of confidence algorithms provide p-values and calls that measure the confidence in detection, or, change, of the specific target RNA. Each algorithm has its own mathematical basis; the quantitative algorithm uses a robust estimator of the mean difference in probe pair intensities, while the confidence algorithm uses rank-based (non-parametric) methods to generate p-values.
Due to the complexity of raw hybridization data, the two algorithms can generate results that appear discordant. For example, the Signal Log Ratio may be greater than 1 but the call may be No Change. Such a result indicates that despite an overall change in the intensity of the probe set, the patterns of individual probe pairs do not detect a target-specific change with high confidence. A stringent analysis strategy combines both types of output. For example, a query of comparison data for all probe sets with Increase calls AND a Signal Log Ratio greater than 1.
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