I run enrichR on a seurat object (spatial) that contains two different tumor-subtypes in two distinct regions of the sample. The below enrichment analysis yields an overlap between the positive and negative markers (Angiogenesis and Apoptosis). Do I miss something conceptually or is this a bug / what might cause this type of behavior? Changing the p-value changes the output only slightly, but this overlap remains. If I use a different test (e.g. t-test), Apoptosis still remains a duplicate.
I run enrichR on a seurat object (spatial) that contains two different tumor-subtypes in two distinct regions of the sample. The below enrichment analysis yields an overlap between the positive and negative markers (Angiogenesis and Apoptosis). Do I miss something conceptually or is this a bug / what might cause this type of behavior? Changing the p-value changes the output only slightly, but this overlap remains. If I use a different test (e.g. t-test), Apoptosis still remains a duplicate.
DEenrichRPlot( Sobj_Out, ident.1 = "Tumor_s2", ident.2 = "Tumor_s3", balanced = TRUE, logfc.threshold = 0.25, assay = "Spatial", max.genes=500, p.val.cutoff = 0.3, enrich.database = "MSigDB_Hallmark_2020", num.pathway = 30 )