So the Ct value should be independent on the increased number of cycles right, whereas the RFU will increase further and thereby not be a direct measure of what is in the sample. So what is a potential ratio of 1:2 ref and target gene could be seen as as 1:5 after x number of cycles using the RFU because of the higher amplification of more abundant gene.
Correct - google delta delta Ct.
However if one would establish standard curves prior to measuring of samples, the two values could both be used right?
Only if the efficiency of the reactions are equal, if I have it right. it's about 8 years since I last did qPCR, so I'm a bit behind on how things work now.