Accurate and robust prediction of patient's response to drug treatments is critical for developing precision medicine. However, it is often difficult to obtain a sufficient amount of coherent drug response data from patients directly for training a generalized machine learning model. Although the utilization of rich cell line data provides an alternative solution, it is challenging to transfer the knowledge obtained from cell lines to patients due to various confounding factors. Few existing transfer learning methods can reliably disentangle common intrinsic biological signals from confounding factors in the cell line and patient data. In this paper, we develop a Coherent Deconfounding Autoencoder (CODE-AE) that can extract both common biological signals shared by incoherent samples and private representations unique to each data set, transfer knowledge learned from cell line data to tissue data, and separate confounding factors from them. Extensive studies on multiple data sets demonstrate that CODE-AE significantly improves the accuracy and robustness over state-of-the-art methods in both predicting patient drug response and de-confounding biological signals. Thus, CODE-AE provides a useful framework to take advantage of in vitro omics data for developing generalized patient predictive models. The source code is available at https://github.com/XieResearchGroup/CODE-AE.