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msraredon / NICHES

Niche Interactions and Cellular Heterogeneity in Extracellular Signaling
https://msraredon.github.io/NICHES/
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question about result meaning? #10

Closed jinyuanchun closed 1 year ago

jinyuanchun commented 1 year ago

thank you for your great packages. i use it in my project. i want to know the meaning of result? image

msraredon commented 1 year ago

I'm not entirely sure that I recognize correctly what you are posting, but if this is a screenshot of the NICHES CellToCell output matrix, transposed for python workflows, and your question is about the meaning of the numeric values:

These values are the product of ligand module expression on the sending cell with receptor module expression on the receiving cell. It is a proxy for 'connective intensity'. Scaling these values by mechanism (here, by column) will yield values reflecting z-scores within the dataset.

Statistical tests can be run on either the starting values or on scaled values to determine significance for a given question. We recommend following/modifying single-cell vignette workflows for these types of tasks, like that explained here: https://satijalab.org/seurat/articles/de_vignette.html

Does this help? Does this answer your question?

S