nolanlab/spade — Issue #23: Include consensus median annotations in .gml files
Author: esimonds
Created: 2012-01-10 03:10:15+00:00
State: open
Labels: feature

Currently SPADE writes out median, fold, and cvs annotations in the .gml files. However, since each .gml file describes a single .fcs file, it can be tough to get a quick overview of how the tree is organized. For example, when you have several .fcs files with low cell numbers, the median values in the nodes tend to jump around a lot as you flip between the files simply due to stochasticity. The general trend is the same, but the cells that get assigned to each node can be quite variable depending on the random chance of cells that got acquired in that file, and also the pattern of staining on each particular file.

I thought it might be a good idea to write out one more set of .gml files called "consensus.fcs.density.fcs.cluster.fcs.medians.gml". This would contain the median value of each parameter in the downsampled dataset. These values already calculated anyway.