Increasing the timeout is one option, however I would also suggest considering an approach that would build your arrays over multiple frames, that is splitting the work up into separate jobs. As long as you give control back to the Flash Player every once in a while, you will not get this exception.
I'm not certain of the specifics of your problem, however you will need to find a way to parallelize or just simply segment your calculations. If your algorithm centers around one major loop, then consider creating a function that takes all of the arguments necessary to record the context of a single iteration. Then, create a simple control loop that will call this function and determine when to wait until the next frame and when not to. Leveraging AS3 closures can also help with this.