Comments (5)
MikeDMorgan
commented on August 10, 2024
It 100% depends on your research question - Milo is agnostic to the modality.
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deconvolute
commented on August 10, 2024
I am getting two extreme results while running Milo with RNA and Integrated assay.
Results from Integrated assay:
Results from RNA assay:
Please let me know your thoughts on it.
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MikeDMorgan
commented on August 10, 2024
Clearly these are 2 completely different graphs - this has nothing to do with Milo.
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AteeqMKhaliq
commented on August 10, 2024
Hi Mike, This is what we got when we ran milo, we got two different results on the same cells!
Dr Ateeq Khaliq
IUPUI, Indiana.
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MikeDMorgan
commented on August 10, 2024
Hi @AteeqMKhaliq - these are 2 different NN-graphs, that means the underlying connectivity and thus neighbourhood composition is different. It doesn't matter that these are the same cells. Again, this is a function of the data, and the multi-modal integration, not Milo or differential abundance testing. I suggest you examine the differences in the integration to resolve this conundrum.
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Related Issues (20)
- Lack of Robustness to Missing Values in Dependent Variable HOT 3
- Cell Condition Relabelling Functionality HOT 3
- Prevention of Neighbourhood Merging of Similar Cell Types into Neighbourhood Groups HOT 1
- Cell type is lost during annotateNhoods HOT 5
- Function Not Found Error HOT 3
- nhood size distribution: some neighbourhoods have over 2000 cells HOT 4
- Progress Bar for GLMM HOT 6
- object 'as.SimpleList' of mode 'function' was not found when running calcNhoodDistance HOT 2
- Multiple comparisons gives identical results by using model.contrasts HOT 12
- Does MiloR take into account that the two compared conditions have different number of cells? HOT 2
- Log10 FC or Log2 FC? HOT 1
- How to use MiloR after subsetting the cell types from total cell types? HOT 4
- Direction of test for logFC calculation HOT 1
- Existence of 2 tuitorials for the "Differential abundance testing with Milo - Mouse gastrulation example" HOT 3
- Import precomputed graph HOT 7
- makeNhoods graph refinement (issue with isolated vertices) HOT 4
- No Significant Neighbourhoods Result is Error HOT 1
- Mass cytometry data HOT 1
- MiloR in spatial transcriptomics data HOT 1
- Gene expression testing of only DA neighborhoods within group?? HOT 3
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