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Danko-Lab / BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression
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select.marker can't return marker genes of stromal cells #37

Open SerendipityCreate opened 1 year ago

SerendipityCreate commented 1 year ago

when I check the result of function select.marker, sc.dat.filtered.pc.sig, I found it return all rows of NA in stromal cells, while other cells didn't. How to solve it? thanks you!

tinyi commented 1 year ago

Dear user,

Thank you for your interest in our methods.

One possibility could be that no genes showed significant differential expression for stromal cells, which can be caused by 1) too few number number of stromal cells, 2) the presence of other cell types of similar transcription profile. You can try lowering the cutoff in select.marker.

Best,

Tinyi

On Tue, May 23, 2023 at 5:53 AM YaoTian @.***> wrote:

when I check the result of function select.marker, sc.dat.filtered.pc.sig, I found it return all rows of NA in stromal cells, while other cells didn't. How to solve it? thanks you!

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