How to Use t-SNE Effectively

Re:How to Use t-SNE Effectively by daemonk on Sunday October 16, 2016 @08:05AM (#12718237)

The seurat R package (http://satijalab.org/seurat/) tries to give you more information on how to choose your PCs. But as with anything in biology, it becomes subjective at some point.

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Re:How to Use t-SNE Effectively by lasso1 on Sunday October 16, 2016 @08:38AM (#12718338)

Thanks!

I happen to have some super high-dimensional data (~100k-1m dimensions), which takes a huge amount of time to work with because i have to custom write everything, and i notice they claim all their underlying functions use sparse matrix representations. Have you tried it in a very high dimensional context?

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Re:How to Use t-SNE Effectively by daemonk on Sunday October 16, 2016 @09:52AM (#12718574)

With single cell data, gene expression data from each cell is considered a dimension. So you end up with something in the range of 20-30k genes and possibly thousands of cells (~25k x thousands matrix). I don't think the technology is at the scale of hundreds of thousands of cells yet. So I am not sure if this package will handle 100k-1m dimensions.

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