I am having four treatment (treatment A , treatment B, treatment C and treatment D) and I have calculated relative fold change(2^delta delta ct) values of the gene of interest using delta delta ct method normalized with housekeeping gene and relative to control. The treatment A is taken as control and other treatments as experimental. Now I need to do ANOVA on this data. I am confused regarding the use of fold change data directly for statistical analysis (ANOVA). I have seen in many paper that they use delta Ct value directly for statistical analysis or log2 fold change data. Many people say that use of fold change value directly for statistical analysis is wrong. So I am really confused which data to apply to do ANOVA.

Can anyone please explain me how and which data is needed to be used for ANOVA with an example?

Also is there any way to use fold change value directly for statistical analysis.

My Fold change values are something like given below:

Treatment                          Fold_change   Mean _Fold_change   Std_Dev                                                                                                       

Treatment A (Replicate 1)                    1

Treatment A (Replicate 2)                    1                       1                       0

Treatment A (Replicate 3)                    1

Treatment B (Replicate 1)                    3.1                                          

Treatment B (Replicate 2)                    2.5                   2.83                  0.31

Treatment B (Replicate 3)                    2.9

Treatment C (Replicate 1)                    0.65                                          

Treatment C (Replicate 2)                    0.55                0.48                  0.21

Treatment C (Replicate 3)                    0.25                                                       

Treatment D (Replicate 1)                    0.25                                        

Treatment D (Replicate 2)                    0.33                0.29                 0.04

Treatment D (Replicate 3)                    0.29

Relative fold change value were calculate by 2^ delta delta Ct with treatment A as control.