p-value Distribution of Random Cell Types Peaks At Zero And Half And One

jinworks / CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

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p-value Distribution of Random Cell Types Peaks At Zero And Half And One #149

Open DarioS opened 2 months ago

DarioS commented 2 months ago

I randomised the cell types by allHuman$cellTypeRandom <- factor(sample(LETTERS[1:5], ncol(allHuman), replace = TRUE)). However, the p-value distribution still appears to have signal in it, which is unexpected. Also, the distribution looks trimodal (0, 0.5, 1).

sqjin commented 2 months ago

@DarioS While this is unexpected at the first glance, I think this is possible because some L-R pairs may still exhibit differential expression and uneven expression levels across cell types. You may also test other cell-cell communication tools to see if this issue exists.

DarioS commented 3 weeks ago

Looking at the MultiNicheNet vignette, it meets distributional expectations. Perhaps such quality control plots are a feature that is missing from CellChat.