I always understood fold change calculations following a qPCR to be calculated by 2^-(ddCT). Is this incorrect, my mentor thinks it is? Potentially they are thinking of something else. Could you please include literature mentioning the correct way to calculate fold change. 

I ran a co-culture experiment with HeLA cells and bacterial members common of the vaginal microbiota. I used siRNA to knockdown LAMP3 antiviral gene.

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