Hi everyone, I'm clustering my single-cell data using Scanpy package, and I use rank_gene_groups to rank genes for characterizing groups. This returns names, scores, logfoldchanges, and pvals_adj for my Anndata format. I'm trying to interpret scores for this data, but I couldn't find any information except their source code. The values for scores are usually between about 1.2 to 39. This range doesn't make sense based on their definition, as below:
scores: structured `np.ndarray` (`.uns['rank_genes_groups']`) Structured array to be indexed by group id storing the z-score underlying the computation of a p-value for each gene for each group. Ordered according to scores.
A couple of lines from my result is shown as follows. 0-n means the 'name' of cluster 0, followed by 0_s as 'scores', 0-p as 'pvals_adj', and 0_l as 'logfoldchanges' for cluster 0. Afterward, we have the same data for other clusters. (I have 5 clusters, but not all are shown in the image)
Could you please tell me what "scores" really mean in this result? Your help would be much appreciated! Thanks a lot in advance!