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In this paper, we study training based channel estimation for relay networks using the amplify-and-forward (AF) transmission scheme. We first point out that separately estimating the channel from source to relay and the channel from relay to destination incurs several problems. We then propose a new estimation scheme that directly estimates the overall channel from source to destination. The proposed channel estimation well matches the AF based space time coding that was developed recently. Both linear least-square estimator and minimum mean- square-error estimator are studied. The corresponding optimal training sequences and the optimal precoding matrices are also derived.