We consider multi-antenna wireless systems aided by large intelligent surfaces (LIS). LIS presents a new physical layer technology for improving coverage and energy efficiency by intelligently controlling the propagation environment. In practice however, achieving the anticipated gains of LIS requires accurate channel estimation. Recent attempts to solve this problem have considered the least-squares (LS) approach, which is simple but also sub-optimal. The optimal channel estimator, based on the minimum mean-squared-error (MMSE) criterion, is challenging to obtain and is non-linear due to the non-Gaussianity of the effective channel seen at the receiver. Here we present approaches to approximate the optimal MMSE channel estimator. As a first approach, we analytically develop the best linear estimator, the LMMSE, together with a corresponding majorization-minimization based algorithm designed to optimize the LIS phase shift matrix during the training phase. This estimator is shown to yield improved accuracy over the LS approach by exploiting second-order statistical properties of the wireless channel and the noise. To further improve performance and better approximate the globally-optimal MMSE channel estimator, we propose data-driven non-linear solutions based on deep learning. Specifically, by posing the MMSE channel estimation problem as an image denoising problem, we propose two convolutional neural network (CNN) based methods to perform the denoising and approximate the optimal MMSE channel estimation solution. Our numerical results show that these CNN-based estimators give superior performance compared with linear estimation approaches. They also have low computational complexity requirements, thereby motivating their potential use in future LIS-aided wireless communication systems.