Determine two sets of samples being independent by fisher exact test method

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I am using Matlab to determine two sets of samples being independent by fisher exact test method. Now I have generated 1000 samples for both random variables, and I already used reject-accept sampling method (different envelopes) to get the observed rejection and acceptance counts. For example, the total samples number is a, the observed rejection for first random variable is b, and observed acceptance will be a-b. The observed rejection for second random variable is c, and observed acceptance will be a-c. So how do I know these two samples are independent?