5.3.5 seurat 的几种findmaker比较

from : https://www.biostars.org/p/409790/

  • FindMarkers will find markers between two different identity groups - you have to specify both identity groups. This is useful for comparing the differences between two specific groups.

  • FindAllMarkers will find markers differentially expressed in each identity group by comparing it to all of the others - you don't have to manually define anything. Note that markers may bleed over between closely-related groups - they are not forced to be specific to only one group. This is what most people use (and likely what you want).

  • FindConservedMarkers will find markers that are conserved between two groups - this can be useful if you want to find markers that are conserved between a treated and untreated condition for a specific cell type or group of cells. It means they are differentially expressed compared to other groups, but have similar expression between the two groups you're actually comparing.



Idents(object = sce) <- sce@meta.data$'celltype'
# 然后再往下走find流程
sce.markers <- FindAllMarkers(object = sce, only.pos = TRUE, min.pct = 0.25, thresh.use = 0.25)