Correct usage of FindConservedMarkers() in Seurat

0

Entering edit mode

3.0 years 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 • 3.3k views

ADD COMMENT • link updated 3.0 years ago by antonioggsousa 3.2k • written 3.0 years ago by almogangel • 0

1

Entering edit mode

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

ADD REPLY • link 3.0 years ago by antonioggsousa 3.2k

Login before adding your answer.