Hello, I have problems using “rank_gene_groups”.
Even if I already logarithmized my data with scanpy.pp.log1p function, the following warning sign appears when I try to run wilcoxon test.
WARNING: It seems you use rank_genes_groups on the raw count data. Please logarithmize your data before calling rank_genes_groups.
Generally the test is performed on adata.raw if present. I would assume your raw data is not logarithmic. You can explicitly set use_raw=False.