Finding cluster specific markers in the Seurat object
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5 weeks ago
ahmad mousavi ▴ 550

Hello

I have a basic question, I have done found top marker in the Seurat object, however using Violin plot shows this marker are not specific for the clusters. I used average expression function but it couldn't help me for this goal.

How can I find the most specific markers in each cluster?

thanks.

sequencing seurat scRNA scRNA-SEQ • 236 views
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It's hard to say without seeing plots. But you should check the params for FindAllMarkers, you can set LFC threshold, or change the test type itself. For example, you could use MAST.

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yeah you are right , but for example checking 500 violin plots, is a time consuming task !!

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