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jinworks / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
GNU General Public License v3.0
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P.value threshold 1 in identifyOverExpressedGenes #17

Open trnguyenuka opened 11 months ago

trnguyenuka commented 11 months ago

Hello,

thank you for developing a great tool!

I have a question regarding the tutorial "Comparison analysis of multiple datasets using CellChat". In this analysis, why did you set the threshold for p.value to be 1? It's kind of unsual to me to set such threshold, since 0.05 is a commonly used and it would make sense statistically.

Screen Shot 2023-11-21 at 13 32 59

Best wishes H.N

sqjin commented 11 months ago

@trnguyenuka Thanks for pointing it out. It should be the default value thresh.p = 0.05. I think this is a typo when I tweak the different approaches for Wilcoxon test.