Machine learning (ML) started to become widely deployed in cyber security settings for shortening the detection cycle of cyber attacks. To date, most ML-based systems are either proprietary or make specific choices of feature representations and machine learning models. The success of these techniques is difficult to assess as public benchmark datasets are currently unavailable. In this paper, we provide concrete guidelines and recommendations for using supervised ML in cyber security. As a case study, we consider the problem of botnet detection from network traffic data. Among our findings we highlight that: (1) feature representations should take into consideration attack characteristics; (2) ensemble models are well-suited to handle class imbalance; (3) the granularity of ground truth plays an important role in the success of these methods.