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saeyslab / multinichenetr

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
GNU General Public License v3.0
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Interpretation of scaled ligand activity values #35

Closed carolinemorrell closed 10 months ago

carolinemorrell commented 10 months ago

Hi - thanks again for this great tool.

A quick question about the scaled ligand activity value plots.

I have one specific interaction (shown below - wnt5a -fzd6) which looks to be upregulated in my negative group on the absolute values, but then in the scaled value looks to have exactly the same values for up and down in both groups. I am not sure how to interpret this - are you able to shed any light?

Thanks

Caroline

image

browaeysrobin commented 10 months ago

Hi @carolinemorrell

You can read more about the interpretation in this issue: #33

Short answer: scaled activities represent the ranking of that ligand compared to other ligands in having target gene enrichment; unscaled values represent absolute enrichment. The higher the absolute enrichment, the more trustworthy, but we have encountered many situations with good ligand rankins (thus looking at scaled ligand activities) even though absolute enrichment was quite low.