My Results have both CT values and Calculated concentration values among these two which should I consider for the statistical analysis. Also how to calculate the increase or decrease in folds.
If you have calculated concentrations I assume that you used external standardization. If so, it's better to use the calculated concentrations as these account for the amplification efficiencies of your assays.
The relative change is the ratio of two concentrations. Are you asking how to do a division?
Regarding the statistical analysis: concentrations are approximately log-normal distributed. If you use a method that assumed normal distribution, then use the logarithms of the concentrations for the statistical analysis. Note that the (arithmetic) mean of log(X) is the logarithm of the geometric mean of X. If you want to estimate arithmetic means, you will have to use a statistical model based on the lognormal or, approximately, on the gamma distribution. It's also possible to use a quasi-Poisson model (if you don't need a proper likelihood, AIC, BIC and alike).
https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/926410/Understanding_Cycle_Threshold__Ct__in_SARS-CoV-2_RT-PCR_.pdf
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