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How to quantify the data by using the efficiency and CT generated by Miner.

In most case, we recommend to use the average efficiency of each gene and the average CTs of each replicates (replicates from the same sample, or "PCR replicates") to do quantification. While when you concerned the tissue or treatment specific inhibitory or activatory effect of PCR reaction for the same gene in your experiment, you might need to use the average efficiency of replicates instead of the average efficiency of each gene. But in this case, you had better use more replicates (6 or more) for each group to get accurate average efficiency from replicates because you have fewer samples to do the average (like only three if you do triplicates). Here is an example in Excel file for how to do the quantification using the average efficiency of each gene and the average CT of replicates.