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I would like to use both in my sentence. However, I really confused about it. I fell that it is incorrect.

For example,

The number of variables in both simulation and real data is fixed to five variables.

Is my sentence correct?

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Almost!

The number of variables in both of the simulations and in the real data is fixed to five.

You don't need to declare variables again at the end of the sentence if you have already mentioned it. I'm assuming here you have two simulations (both) AND some real world data.

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