Wed Dec 03, 2014 8:03 am by petterbrodin
Dear Elyse, good question.
These tools represent two broad approaches for exploring data, clustering (SPADE) and dimensionality reduction (PCA and SNE).
PCA and SNE both perform dimensionality reduction, but in different ways. Simply put, PCA performs a linear dim. reduction while SNE performs a nonlinear dim. reduction and due to the nature of cytometry data, SNE therefor tend to produce clearer insights into the underlying structure of the data than PCA does. Both viSNE and ACCENSE use the same SNE algorithm for dim. reduction and visualization. The difference between these tools is that beyond visualization, ACCENSE also allow for an automated classification of cells into subpopulations and the export of such data in a tabular format for statistical analyses.
SPADE clusters the data and visualize the clusters on a minimum spanning tree, but does not directly support statistical comparisons. Citrus on the other hand, allows for statistical comparisons between samples based on clustering of the data.
I hope this helps!
Petter