some questions about findmarkrs and findallmarker #7946
dd123456000
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this is my code
① levels(pbmc)
[1] "Sertoli cell_IT" "Leydig cell_IT" "Stromal cell_IT" "Macrophage_IT" "Endothelial cell_IT"
[6] "Germ cell_IT" "Blood_IT" "Myoid cell_IT" "T cell_IT" "Plasma cell_IT"
[11] "Sertoli cell_NT" "Stromal cell_NT" "Leydig cell_NT" "Myoid cell_NT" "Germ cell_NT"
[16] "Endothelial cell_NT" "T cell_NT" "Macrophage_NT" "Blood_NT" "Plasma cell_NT"
DEGs <- FindMarkers(pbmc,ident.1 = 'Myoid cell_NT',ident.2 = Myoid cell_IT', verbose = FALSE, test.use = 'wilcox',min.pct = 0.1)
DEGs <- FindMarkers(pbmc,ident.1 = 'Myoid cell_IT',ident.2 = Myoid cell_NT', verbose = FALSE, test.use = 'wilcox',min.pct = 0.1)
Why is it that the results are different after I swapped the IDs?
②levels(pbmc)
"IT' "NT"
DEGs <- FindMarkers(pbmc,ident.1 = 'NT',ident.2 = ‘IT', verbose = FALSE, test.use = 'wilcox',min.pct = 0.1)
pbmc.markers <- FindAllMarkers(pbmc, only.pos = FALSE,min.pct = 0.25, logfc.threshold = 0)
I want to know if these two sets of results will be the same. Also, this is my first attempt at setting 'idents' as groups. I'm wondering if this result is reliable?
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