It depends on which method produced them.
By Cell scores each gene set in each cell. iSCanGuide z-scores every gene within the cell, then compares the genes in your selected set against the genes in all the other sets you selected.
- Enrichment score — average z-score of the set’s genes. Positive means expressed above the cell’s average.
- Score difference — the set’s average z-score minus that of the other selected sets. Tells you whether the set stands out from the rest of your selection.
- p-value — one-sided Welch’s t-test of whether the set’s genes score higher than the other sets’ genes.
Because the reference is the other sets you chose, results are only comparable within a single analysis.
From DE Analysis works at the group level. Genes are ranked using the fold change and p-value from a completed DE analysis, and gene set enrichment analysis is run on that ranking. The enrichment score is the normalized enrichment score for the set; the score difference compares it against the other selected gene sets. Every cell in the group carries the same value, so identical numbers across cells are expected. Use this to assign a function to a cluster or condition.
The UMAP colors cells by enrichment score. All three values are in the downloaded results file.