We are comparing different DNA extraction methods and we use qPCR for analysis. We conducted PCR on 2 amplificators, but they had pretty different results. For example, one of the methods had 30 negative and 10 positive samples on the first amplificator, but only 4 negative samples on the second one. Moreover, it had the highest Cq value on the fisrt one, but the lowest on the second one. What could be the cause of this? We used the same program and reagents for both amplificators.
To clarify, are you using qPCR to measure DNA? It's an unusual, but not unheard of application.
Most folks use qPCR to measure gene-expression from mRNA, not to measure presence/absence/copy number of gDNA.
My guess is that you are looking for presence of a pathogen (e.g. COVID viral RNA)? Are you trying to choose between different sample preparation protocols? What do your controls look like? What is your minimum detection threshold?
If you clarify your question, then we can give more specific advise.
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