Question: What is the Median Normalized Average statistic in Loupe Browser?
Answer: This statistic is used during "Significant Genes" analysis in Loupe Browser. The median-normalization average (MNA) of a gene in a cluster is calculated as the mean of observed UMI counts normalized by the size factor for each cell in the representative cluster. It is calculated as follows*:
MNA(gene_X) = mean ([gene_X_UMI_count / size_factor for cell in cluster])
where the size factor is computed for every cell as follows:
size_factor = (total_UMI_counts_in_current_cell / median_UMI_counts_per_cell)
For example, if a library has 1000 cells, then 1000 different size factors are calculated.
This calculation becomes apparent in the Loupe Browser when a user chooses between locally distinguishing and globally distinguishing categories of differential gene expression. For globally distinguishing, median UMI count is calculated over all cells in the library. For locally distinguishing, it is calculated over the selected cluster subset. Thus the number of cells being considered changes in the size factor estimates.
* In Space Ranger all calculations are based on spots instead of cells.
Products: Single Cell Gene Expression, Spatial Gene Expression, Loupe Browser
Additional information:
Related KB article: How is "Log2 fold change" calculated?
To explore the code on your own, please see our Github repository here. Disclaimer: Source code for 10x pipelines is available at https://github.com/10XGenomics for interested customers. However, 10X Genomics is not staffed to answer questions about it or provide support for modifications.