I am going through scanpy tutorials for the first time and don’t understand how to interpret parts of the differential gene expression dotplot of logfoldchange from their plotting tutorial (I did not generate this, it’s a screenshot from the tutorial).
What I don’t understand is why cluster 1 compared with cluster 1 (and all along the diagonal) has logfoldchange values that are nonzero. I assumed that logfoldchange was calculated more or less as follows: log(mean_gene_expression_cluster_A/mean_gene_expression_cluster_B), or for log2foldchange: log(mean_gene_expression_cluster_A/mean_gene_expression_cluster_B)/log(2). If we’re comparing exactly the same values, wouldn’t log(1)=0 result in zeros along the diagonal?
Thanks! I appreciate any input.
