Question: In Loupe Browser, why is the average in Feature Table different from the mean in Violin Plots?
Answer: The average value in the Feature Table is “Median Normalized Average”, which is explained in this article: What is the Median Normalized Average statistic in Loupe Browser?
For Violin Plot, when selecting ‘Linear’ in the ‘Scale & Attribute’ parameters in the Active feature list, the mean value in the Violin Plot is the average UMI count in each cluster without normalization. For more details on different parameters, please check out this page: navigating the Loupe Browser user interface.