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Is it reasonable to use DiffusionMap with n_pcs = NA?

Open sam-israel opened this issue 7 months ago • 1 comments

The help page on DiffusionMap says that using e.g. 50 PCs results in more regular looking diffusion maps. First, I would like to ask - it results in more regular looking diffusion maps compared to what ?

Second, Is it reasonable not to use projections for the diffusion map (n_pcs=NA), in case that the result looks more reasonable biologically ?

sam-israel avatar Nov 21 '23 13:11 sam-israel