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The authors thank Andrea De Biase of Life Technologies for discussions involving TaqMan probes, quenchers, and general qPCR optimization.
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QPCR optimization was performed using PPARγ plasmid clones.
JM designed and performed PCR assays and assisted in qPCR optimization.
In general, qPCR results were in agreement with the microarray data.
In general, qPCR is quick to perform with a low to medium throughput, since most qPCR platforms have a capability format of 96 or 384 [ 7].
Still, far and above any other single issue regarding one-step qPCR optimization, we are solidly convinced that the most powerful thing one can do to attain ideal (or near-ideal) efficiencies from any qPCR target amplification is run a Test Plate to physically determine which specific RNA dilution ranges work best for each different qPCR target.
Compiler optimizations can be grouped into general optimizations and advanced optimizations.
We first formulate a general multiobjective optimization problem.
A general analysis, optimization, and decision-making method is presented.
We formulate and solve the resulting ML maximization as general convex optimization problems.
Solving the general optimization problem in order to generate the maximally informative input is computationally challenging.
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