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Why FindMarkers between conditions shows pct.1 and pct.2 as 1 for most of the genes?

I have a Seurat object data which has identified seurat_clusters. And there are two conditions treatment and notreatment for this dataset.

I performed DEA between conditions in a specific cluster 3 using the FindMarkers function from Seurat like the following:

## Get the cluster 3 cells 
data2 <- subset(data, subset = RNA_snn_res.0.2 == 3)
Idents(data2) <- "Condition"

all.genes <- rownames(data2)
data2 <- ScaleData(data2, features = all.genes)

DEG <- FindMarkers(data2, ident.1 = "treatment", ident.2 = "notreatment", verbose = FALSE, logfc.threshold = 0, min.pct=0)
head(DEGs, n = 10)

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Could you please tell me why pct.1 and pct.2 are 1 for all the genes above?

seurat findmarkers scrna-seq
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updated by Ram Ram • written by Biologist Biologist

1 answer

For pct.1 and pct.2, please check in this link.

For Doheatmap in seurat, you can absolutely define the features (genes of your interest). For this please check here.

• 0 views • link
written by bk11 • bk11

I know pct.1 and pct.2, my question is why there is 1 for all the genes of pct.1 and pct.2?

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written by Biologist Biologist

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