SPADE (Spanning-tree Progression Analysis of Density-normalized Events) is a clustering algorithm. Its goal is to automatically identify cell populations in multidimensional cytometry data files. FCS Express 6 and later allows users to run SPADE on Flow, Mass and Image cytometry data.

More details on SPADE can be found in the following publications:

• Qiu, P., et al. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat. Biotech. 29, 886-891 (2011).
  
• Qiu, P. Inferring phenotypic properties from single-cell characteristics. PLoS One. 5, Web (2012).

SPADE and k-Means are examples of clustering algorithms. The goal of the algorithms is to group data (i.e., cells) together in a way that data in the same group (i.e., the same cluster) are more similar to each other than data from other groups (i.e., other clusters). With respect to k-Means, SPADE includes a series of computational steps that:

• Allow rare events to form their own clusters instead of being outnumbered by abundant cell populations during clustering.
• To generate a minimum spanning tree representation in which clusters are connected with minimum total edge length. t-SNE and PCA are examples of dimensionality reduction algorithms. A dimensionality reduction algorithm attempts to map high-dimensional data into lower dimensions by finding a data set in low-dimensional space that, in some way, represents the original high-dimensional data.

There are many reasons to choose FCS Express to run the SPADE transformation:

• The user interface that allows users to run SPADE in FCS Express is very intuitive and easy to use.
• SPADE analysis in FCS Express is completely integrated with the layout, meaning that the user can draw gates on SPADE plots to select one or multiple nodes for downstream analysis. Similarly, gates drawn on classical dot plots can be applied to SPADE plots as well.
• SPADE is extremely fast in FCS Express, as the team at De Novo Software made great efforts to enhance running of the algorithm and the software in general.

Check out our recorded webinar below to see why you should be Using SPADE and data transformation tools in FCS Express!