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how to use delta-delta Ct method? - when no expression in healthy controls! (Jan/20/2011 )

for me it is not clear, how to use the delta-delta Ct method, if my healthy controls not expressing this special gene (e.g. tumor marker)? I normally use a 45 cycle real time protocol, and some markers are undetermined.

hope tho get any suggestions, how to solve the problem,
thx

-moljul-

You can insert maximal cycle number (45 in your case)as Ct value for non-expressing cells and proceed as usual.

-ElHo-

thx for recommendation.

another question arose: can I built a mean value of the delta Cts of all healthy controls to generate the delta delta ct for all samples (healthy & cancer patients)? = delta Ct of one sample minus the mean of the delta Cts of the healthy controls?

-moljul-