How to interpret marker_score N/A

[Eric]

After running marker_check, I see that many of my markers are marked as "OK - marker_score N/A". Here is an example:

(In this case, I have indicated that CD3D, E, and G are not expressed in B cells, and similarly for NCAM1, IL2RA, and CD2 for the Naive T cells.)

How should I interpret that? Does this mean I should drop these markers or might it mean something else?

(Note that I am using monocle3 and the corresponding branch for garnett) 

Thanks!

-Eric

[Hannah A Pliner]

Hello,

Sorry for the confusing messages - because of the way the marker scores are calculated, negative markers don't get a score - it has to do with the fact that it's an absence, so it can't 'conflict' with other markers. They're good to keep.

Best,

Hannah

Hannah Pliner, Ph.D.

Lead Data Scientist for Single Cell Genomics

Brotman Baty Institute for Precision Medicine

Health Sciences Building (HSB) H564E

Seattle, WA

206-616-0454

hpl...@uw.edu

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[Eric]

Ahhh...I get it. Makes sense.  Thanks!