FindAllMarkers pct1 and pct2
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Entering edit mode
16 months ago
Morris_Chair ▴ 230

Hello guys,

I have a doubt about the output of FindAllMarkers, I know that pct.1 is the percentage of features "A" in cluster 1 but I am not sure about pct.2,

Is it the percentage of that features "A" in all the other clusters ? since I am comparing one vs the rest?

object.markers <- FindAllMarkers(object = myobject,only.pos = TRUE, min.pct = 0.25, thresh.use = 0.25)


Thank you

RNA-Seq Seurat • 1.4k views
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Entering edit mode
16 months ago

I'm not really following what you're talking about with pct1 and pct2, but the min.pct parameter just determines the fraction of cells in either group the feature has to be expressed in to be included in the analysis. It's meant to remove lowly expressed genes. So in your case, that'd mean for a gene to be included in the differential expression for cluster 1 (or 2, 3, etc) versus the other clusters, at least 25% of cells in cluster 1 or all other clusters must express the gene.

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Entering edit mode
8 months ago
pnrmm ▴ 20

FindAllMarkers function helps to identify gene markers for each cluster relative to all other clusters. The expression for a given gene among cells in a given cluster is compared against the expression of that gene among cells in all other clusters. In the output, pct.1 is the percentage of cells in the cluster where the gene is detected, while pct.2 is the percentage of cells on average in all the other clusters where the gene is detected. A gene to be considered as an IDEAL cluster marker is expected to be expressed exclusively in that cluster and silenced in all others and thus pct.1 will be more towards 1 and pct.2 towards 0.