Measuring student learning is a complicated but necessary task for understanding the effectiveness of instruction and issues of equity in college STEM courses. Our investigation focused on the implications on claims about student learning that result from choosing between one of two commonly used methods for analyzing shifts in concept inventories. The methods are: Hake's gain (g), which is the most common method used in physics education research and other discipline based education research fields, and Cohen's d, which is broadly used in education research and many other fields. Data for the analyses came from the Learning Assistant Supported Student Outcomes (LASSO) database and included test scores from 4,551 students on physics, chemistry, biology, and math concept inventories from 89 courses at 17 institutions from across the United States. We compared the two methods across all of the concept inventories. The results showed that the two methods led to different inferences about student learning and equity due to g being biased in favor of high pretest populations. Recommendations for the analysis and reporting of findings on student learning data are included.