you mean -ΔΔCt？you could use either -ΔΔCt or the fold change ( 2 to the power of -ΔΔCt).

I second Jianfeng Lin's answer. You can use either of them and ultimately compare the result with respect to the control or the untreated sample.

Deta Ct

Statistical analysis should be performed on log2-transformed fold change (i.e., -ΔΔCt) or on ΔCt. The advantage of using ΔCt is that, after running the test on your chosen softwater, the descriptive stats (mean difference, SD, SEM, 95%CI) will be expressed in -ΔΔCt, which you can easily transform to fold change (2^-ΔΔCt) if you wish.

Although the original Livak paper performed stats on fold changes, this parameter tends to deviate from a Gaussian distribution and is only useful for graphic presentation or summary.

Ref.

Article The Ultimate qPCR Experiment: Producing Publication Quality,...

Article Statistical analysis of real-time RT-PCR data

Thanks a lot for all for your kind help.

I would say -ΔΔCt

ΔCt (delta Ct)

Thanks a lot all for your help!!