Question: R package "tsne" and "Rtsne" give different cell clustering results
1
gravatar for Elaine.7
4.1 years ago by
Elaine.710
Elaine.710 wrote:

I was doing cell clustering for single cell analysis and found these two R packages to do t-SNE clustering. According to the description, package "tsne" is a "pure R" implementation of the t-SNE algorithm, while package "Rtsne" is an R wrapper around the fast t-SNE implementation by Van der Maaten. In addition, when I run "Rtsne", I set parameter theta=0.0 which uses a standard t-SNE implementation. I applied these two functions to the same data set with same parameters, but the cell clustering results were not the same. In detail, "Rtsne" clustered two cell types together, while "tsne" completely separated these two cell types. Why do these two functions give such different results?

ADD COMMENTlink modified 4.1 years ago by igor11k • written 4.1 years ago by Elaine.710
1
gravatar for igor
4.1 years ago by
igor11k
United States
igor11k wrote:

Apparently, there may have been a bug in the tsne package, which may or may not be related to what you are seeing. Check the discussion here to see if it applies: https://gist.github.com/mikelove/74bbf5c41010ae1dc94281cface90d32

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ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by igor11k
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