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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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PCA inferred one lineages and umap two lineages #167

Closed FADHLyemen closed 2 years ago

FADHLyemen commented 2 years ago

Hi, when I use PCA in slingshoot, it inferred one lineage and umap inferred two lineage, which one should I take?

kstreet13 commented 2 years ago

With no more information that this, I cannot recommend one over the other. The question of which dimensionality reduction to use for any given task is largely an open question. For scRNAseq, this paper would probably suggest using PCA or semi-supervised dimensionality reduction.

FADHLyemen commented 2 years ago

Thank you @kstreet13 this is very helpful