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PowerNest is a software tool enabling experimenters to explore the effect of sampling on noise propagation throughout qPCR assays. The sampling process is assumed to be comprised of a number of levels; the acquisition of a sample and the preparation of extracted material, reverse-transcription of the mRNA, and the qPCR itself. Given a small set of data, representative of a larger assay, the error at each stage of the experiment is profiled using a nested-ANOVA.

Armed with this information, PowerNest allows the experimenter to explore the effects of modifications to the experimental design on the expected total error of the assay. When given the financial cost of replicates at each level, PowerNest will calculate a cost-optimal sampling-plan, delivering an experiment design that will minimise processing error and maximise the statistical resolution of the assay.