Correct usage of FindConservedMarkers() in Seurat
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6 weeks ago
almogangel • 0

Dear all,

I have a Seurat object of a certain cell type with a UMAP of 7 clusters. I also have information about the sample's origin (primary tumor/metastatic) in my metadata.

Looking at the UMAP I can clearly see that clusters 1 and 5 correspond to metastatic and the other to primary. I wonder if this is the correct way to identify markers genes for those groups:

FindConservedMarkers(nsclc.mac, ident.1 = c(1,5), ident.2 = c(2,3,4,6,7), grouping.var = "stage")


Thanks!

FindConservedMarkers scRNA-seq Seurat • 198 views
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Hi,

Yes, it sounds good to me, if your aim is to find the conserved markers between metastatic clusters (1 and 5) and the remaining clusters (2,3,4,6,7) across the grouping.var stage.

Other similar functions exist to find differentially expressed genes between sets of class identities as described in this post: FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat

António