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theislab / destiny

R package for single cell and other data analysis using diffusion maps
https://theislab.github.io/destiny/
GNU General Public License v3.0
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Is it reasonable to use DiffusionMap with n_pcs = NA? #64

Open sam-israel opened 7 months ago

sam-israel commented 7 months ago

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 ?

RamRS commented 6 months ago

Also asked on bioinformatics SE: https://bioinformatics.stackexchange.com/questions/21937/using-diffusion-map-on-normalized-or-pca-reduced-data