MultiNicheNet Tutorial Confusion: Which One for Unpaired but Big Data?

[ManyeeLui]

I'm trying to figure out which MultiNicheNet tutorial is the right fit for my data.

I noticed the recommended link for "Condition A vs Condition B - without repeated subjects" actually leads to a file named pairwise_analysis_MISC.knit.md.

Could you please clarify if this vignette is intended for independent, unpaired samples (as the title suggests), or if the term "pairwise" implies it should only be used for paired/matched samples? This distinction is crucial for our statistical model selection.

If we have a large cohort of samples that are strictly independent and non-matched (unpaired), which specific vignette on the main page would you recommend we follow?

[maartenciers]

The pairwise stands for the two specific experimental conditions you want to compare and has nothing to do with the samples. So the "Condition A vs Condition B - without repeated subjects" vignette is the one you want. If you have paired samples then you should pass covariates = "patient"