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delta-delta-Ct method - what to do, when no expression in healthy control? (Dec/21/2010 )

how could i apply the delta-delta-Ct method to my real time PCR results, when target gene (gene of interest) is not expressed ("undetermined") in my healthy control?
is it allowed to insert Ct 45, to complete the formula??



You can replace it with Ct=40 (max number of cycles). I use RealTime StatMiner software and it does it automatically. You can set a filter to see how many times this appeared Undetemined amongst your biological replicates. Undetermined may also suggest you don't have anything in your control, so that may be significant. You just have to setup your filters.

Take a look at this PCR whitepaper http://www.integromi...qPCR_Statistics

and also the Livak paper.