Comments (3)
Hi @hai178912522,
It makes perfect sense to use the Harmony dimensionality reduction for constructing the KNN graph, if this is the integration methods you have been using for other graph based analyses on your dataset (e.g. clustering, UMAP). This looks like a fairly standard case where no significant differences in abundance are detected, probably because of a small number of replicates per condition (3 replicates as far as I can tell).
One caveat with using Harmony is that it tends to overcorrect differences between samples, as opposed to other integration methods, so it might be that differences between conditions are lost after integration.
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This is the situation with my design. It is a comparison of 8 vs 22 in total。
A data.frame: 30 × 2
sample group
P30.post.1 P30.post.1 Post-treatment
P2.pre P2.pre Treatment naive
P29.pre P29.pre Treatment naive
P29.post.1 P29.post.1 Post-treatment
P37.post.1 P37.post.1 Post-treatment
P8.pre P8.pre Treatment naive
P38.post.1 P38.post.1 Post-treatment
P26.pre P26.pre Treatment naive
P14.pre P14.pre Treatment naive
P9.pre P9.pre Treatment naive
P7.pre P7.pre Treatment naive
P4.pre P4.pre Treatment naive
P15.pre P15.pre Treatment naive
P27.pre P27.pre Treatment naive
P22.pre P22.pre Treatment naive
P1.post.3 P1.post.3 Post-treatment
P33.post.1 P33.post.1 Post-treatment
P12.pre P12.pre Treatment naive
P36.post.1 P36.post.1 Post-treatment
P34.pre P34.pre Treatment naive
P6.pre P6.pre Treatment naive
P23.pre P23.pre Treatment naive
P33.pre P33.pre Treatment naive
P20.pre P20.pre Treatment naive
P35.post.1 P35.post.1 Post-treatment
P17.pre P17.pre Treatment naive
P30.pre P30.pre Treatment naive
P18.pre P18.pre Treatment naive
P35.pre P35.pre Treatment naive
P28.pre P28.pre Treatment naive
Is there any good method to help adjust the results?
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Closing due to inactivity
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Related Issues (20)
- 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
- Can you implement a complete miloR in python ? HOT 1
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