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satijalab / seurat-data

Dataset distribution for Seurat
GNU General Public License v3.0
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VlnPlot shows several perfectly lines of cells. #39

Closed levinhein closed 3 years ago

levinhein commented 3 years ago

Hello,

As you can see on below VlnPlot, you will notice that cells seem to be aligning perfectly along the same gene expression value across all cell types.

Is this abnormal? What's the likely reason and do you have any recommendations???

VlnPlot(immune.combined.sct, features = "NAMPT", pt.size = 0.2, ncol = 1) + NoLegend()

image

andrewwbutler commented 3 years ago

This is a question probably more appropriate for the main seurat github repo so if you have further questions I would recommend posting there. My guess, given that I don't know what data this is or how you processed it, is that you haven't normalized it and the "lines" of expression correspond to UMI counts of expression for this gene.