Question: How is the "Log2 Fold Change" value calculated in Cell Ranger and Loupe Cell Browser?
Answer: The "Log2 Fold Change" value reported in Cell Ranger and in the gene table in Loupe Cell Browser is the ratio of the normalized mean gene UMI counts in each cluster/group relative to all other clusters/groups for comparison.
In Loupe Cell Browser, the comparison is between a cluster/group versus the rest of the dataset (globally distinguishing) or versus all other checked groups in a selected category (locally distinguishing).
For more specifics on how the value is calculated, please see the Cell Ranger source code for the differential expression analysis module:
# Introduce a pseudocount into log2(fold_change) 'log2_fold_change': np.log2((1+gene_sums_a)/(1+size_factor_a)) - np.log2((1+gene_sums_b)/(1+size_factor_b))