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I have generated a list of canonical markers for cluster 0 using the following command:

cluster0_canonical <- FindMarkers(project, ident.1=0,  ident.2=c(1,2,3,4,5,6,7,8,9,10,11,12,13,14), grouping.var = "status", 
min.pct = 0.25, print.bar = FALSE)

And I got the following output, but I do not understand why the canonically expressed ribosomal markers seem to be expressed at high levels in both the cells within the cluster AND cells that are NOT in the cluster (i.e. both pct.1 and pct.2 are close to 1, but P value is highly significant). We would not expect this for canonical markers - we would instead expect the genes to be expressed at high levels in the cells within the cluster but at low levels in cells not within the cluster. I don't seem to have such an issue with non-ribosomal genes within cluster 0 and cluster 0 is the only cluster where I get a high number of ribosomal genes as canonical markers.

enter image description here

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Your interpretation of pct.1 and pct.2 is misguided. If pct.1 == 1, the given gene was detected in all of the cells. This carries no information about high expression or low expression in the cell, just that it was detected. avg_logFC is the indication of expression levels. So your expectation, that

"we would instead expect the genes to be expressed at high levels in the cells within the cluster but at low levels in cells not within the cluster"

holds true, as indicated by the positive avg_logFC and significant p-values of the listed RP genes.

Seurat use nautral log, so the FC of RPS6 in cluster 0 vs. all other clusters indicated is 2.718281828459^.55947=1.750.


Seurat FindMarkers() documentation.

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