Teaching science in higher education has traditionally consisted of delivering knowledge as lectures to students following a teacher-centered methodology. The flipped methodology known as inverted instruction can be used as an alternative approach providing a student-centered class. This contribution presents a comparison of two different instruction methodologies, Traditional Instruction Methodology (TIM) and Inverted Instruction Methodology (IIM), in terms of students' perceptions and emotions in a science course. The results after applying various data analytics showed that the IIM had a significant influence in students' perceptions toward the course and made classes more interactive. Besides, the IIM had a positive impact in students' emotions self-reported during the course. In fact, the IIM made a promotion of positive emotions toward the course, particularly when students did not have a prior science educational background. That is especially relevant since the majority of students enrolled had not taken science subjects in the previous educational levels.