Questions tagged [dimensionality-reduction]
The dimensionality-reduction tag has no usage guidance.
3 questions
4
votes
2
answers
415
views
Question about umap using different numbers of pca components as initialization
I am new to the scRNA-seq field and I have been doing some experiments of visualization of UMAP using different numbers of PCA components for initialization. The process involves projecting scRNA-seq ...
- 43
2
votes
1
answer
301
views
Using Diffusion Map on normalized - or PCA reduced data?
This question was also asked on GitHub
In the R package destiny, a Diffusion Map is often performed on the first 50 PCs of the data.
Is there a theoretical reason for performing a Diffusion Map on ...
- 149
0
votes
0
answers
113
views
scRNA: What are good dimensionality reduction/clustering parameters to get biologically plausible groupings?
I've got a moderately large set of PBMCs, over 1M cells. That means I can't easily do a grid search of dimensionality reduction/clustering parameters/methods. Some examples results I'm getting with ...
- 109