Ct values - (Nov/19/2012 )
I think it should be fine as long as you use this same amount of template input for every sample that you are making a comparison with. The expression is all relative anyways.
Housekeeping gene should be idealy from the same cDNA as the target gene, otherwise you are actually measuring different samples. The same is true for the dilutions of the same cDNA. In case there is different concentraton of inhibitors, you could get uneven ratios for undiluted and diluted cDNA.
I would try to limit GAPDH primer concentration to get higher Ct or use a different houseekeping gene that has a lower abundance.
Thank you! I shall try using different endogenous control.