Trouble running Seurat's FindConservedMarkers()
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Entering edit mode
4 months ago
Aaron ▴ 10

I'm trying to run Seurat's FindConservedMarkers() on a cell cluster I have just made with CellSelector():

plot <- DimPlot(seurat_integrated, reduction="umap", label=TRUE) + NoLegend()
myeloid_t_cells <- CellSelector(plot)
Idents(seurat_integrated, cells = myeloid_t_cells) <- "myeloid_t_cells"
mtc_conserved_markers <- FindConservedMarkers(seurat_integrated, ident.1=myeloid_t_cells, 
grouping.var="groups", verbose=FALSE)
write.csv(mtc_conserved_markers, "mtc_conserved_markers.csv")

I have been trying to follow examples online to prevent errors but I am getting an error from the FindConservedMarkers() line and I can't seem to figure out what it means (or how to resolve it):

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.
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AGACGTTTCAGCTGGC-1_1, AGATTGCCAGACGTAG-1_1, AGCTCCTGTAGCGTGA-1_1, 
AGGCCGTGTCTTGTCC-1_1, AGGCCGTTCGGTCTAA-1_1, AGGTCATCACAGGCCT-1_1, 
AGGTCATGTTCCATGA-1_1, ATAACGCAGCGAAGGG-1_1, ATAAGAGGTCTAGCGC-1_1, 
ATCATCTAGTACGCGA-1_1, ATCATCTTCACATGCA-1_1, ATCATGGTCATCTGCC-1_1, 
ATCCGAATCTGGCGAC-1_1, ATCTGCCTCTCGAGTA-1_1, ATGTGTGCAGCCTGTG-1_1, 
ATGTGTGTCAAACCGT-1_1, ATTATCCAGACTTGAA-1_1, ATTATCCGTTCCAACA-1_1, 
CAACTAGTCGGATGTT-1_1, CAAGATCAGTCGTTTG-1_1, CAAGGCCGTTCCAACA-1_1, 
CAAGTTGAGTGTCCAT-1_1, CACACTCAGTTCCACA-1_1, CACCTTGTCCAAACTG-1_1, 
CACTCCAAGCGATAGC-1_1, CACTCCACATGACGGA-1_1, CAGGTGCAGCCCGAAA-1_1, 
CAGTCCTCACATCCGG-1_1, CAGTCCTGTAAACCTC-1_1, CATATTCCAATAACGA-1_1, 
CATCAAGAGAGTACAT-1_1, CATCAGACAGCGAACA-1_1,  [... truncated]
Error in marker.test[[i]] : subscript out of bounds

I have looked around Google and elsewhere on this site - does anyone know how I might resolve it? I would be extremely grateful if someone could help me. Also, I'd be happy to provide any additional data/information if it could be useful.

FindConservedMarkers Seurat • 185 views
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