Entering edit mode
4.3 years ago
david.f.stein
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10
I have a count matrix of single cell data with 122 cells. I am trying to process it with the standard Seurat workflow, however, the UMAP reduction is yielding strange results. Basically, no clusters are forming. I'm wondering if ~100 cells is too low for UMAP. Does anyone know what might be going on here? I can provide my code if necessary
Edit: I found if I raise the "resolution" argument in the "FindClusters" function then clusters are picked up. I'll have to read more about what the "resolution" means in this context.
Did you try "pca" instead of "umap" ?
I ran PCA, TSNE, and UMAP. None seem to result in clusters on visualization
It might be biological then. Did you check what are the top variable genes using function like rowVars ?
I did, finding variable features seemed to work as usual/expected. Is there something I should be looking for in particular? I just saw on a github issue on the Seurat repository that graphical clustering tends to perform poorly for around <100 cells, so maybe I'm just out of luck