Some one asked what tSNE means in a lab meeting, so I made this material as a demonstration about dimensionality reduction and tSNE. Might be useful in the future if some one asks again. tSNE notes:
https://scikit-learn.org/stable/modules/manifold.html#manifold t-SNE (TSNE) converts affinities of data points to probabilities. The affinities in the original space are represented by Gaussian joint probabilities and the affinities in the embedded space are represented by Student’s t-distributions.
The computer treats each gene as a dimension. Gene with similar gene expression will be clustered together. We need to be able to see these clusters in 3 dimensional space so it makes sense to our brains.
Consider running through the notebooks/Dimensions.ipynb to experence the presentation.