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MarioniLab / miloR

R package implementation of Milo for testing for differential abundance in KNN graphs
https://bioconductor.org/packages/release/bioc/html/miloR.html
GNU General Public License v3.0
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No Significant Neighbourhoods Result is Error #342

Closed DarioS closed 1 week ago

DarioS commented 1 week ago

Shouldn't it simply be a message and not an error? Finding no statistically signficant differences seems like a valid outcome to me.

>  groupNhoods(MILOdata, smokerResults)
Error in groupNhoods(MILOdata, smokerResults) : 
  No DA neighbourhoods found

The model specified was ~ Smoker + (1|SampleID)

MikeDMorgan commented 1 week ago

If you set da.fdr=0.1 you can achieve the desired result, i.e. cluster nhoods without any statistically significant DA nhoods.