Regarding Stat Analysis of Randomised Control Clinical Trial

We are in process of analysing data of a Randomised controlled study.

It is challenging to compare the primary endpoints due to difference in methodologies followed in the study & control groups.

In our study, we could determine that was no difference in the pre-test parameters within the study group and control group. However, primary endpoints cannot be compared .
I would like to know if it is ok to only analyse the data of the study group and publish the same.

Please share your thoughts for the same.

Thanks in advance!
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