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I ran FindMarkers twice – once on a subset of cells (subset_cells, where all_cluster == "Neu"), and once on the full Seurat object sc. In both cases, I used:
ident.1 = "T1", ident.2 = "T2"
group.by = "sample"
min.pct = 0
logfc.threshold = 0
test.use = "wilcox" (and added assay = "RNA" in the second call)
Despite these permissive settings (no filtering on expression fraction or log fold change), FindMarkers returned an empty data frame with the warning:"No features pass min.pct threshold; returning empty data.frame"
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I ran FindMarkers twice – once on a subset of cells (subset_cells, where all_cluster == "Neu"), and once on the full Seurat object sc. In both cases, I used:
ident.1 = "T1", ident.2 = "T2"
group.by = "sample"
min.pct = 0
logfc.threshold = 0
test.use = "wilcox" (and added assay = "RNA" in the second call)
Despite these permissive settings (no filtering on expression fraction or log fold change), FindMarkers returned an empty data frame with the warning:"No features pass min.pct threshold; returning empty data.frame"

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