@mihem Yes, so each element along the first axis of your output represents the sample x sample distance matrix implied by one of the cells in the input. So here you would either take the mean across the entire first axis, or if you believe there to be cell-state-specific heterogeneity in the nature of sample effects, you would split the first axis into groups based on, say cell types, before taking the mean and plotting heatmaps for each of those groups. Does that make sense?