R code used in paper "Challenges in the multivariate analysis of mass cytometry data: the effect of randomization.", Cytometry Part A, doi: 10.1002/cyto.a.23908
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Dimensionality Reduction and Phenotyping : folder contains code for reproducing the results shown in Figures 2 and 4 that is, on Dimensionality Reduction (PCA, JIVE, MDS, tSNE) and Cell phenotyping (ensemble clustering)
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Network Reconstruction : folder contains code for reproducing the results shown in Figure 5 and table 1 on network reconstruction analysis (gLASSO, rFCI, RNs)
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For Figure 3 (SPADE results) we used the matlab application of deterministic SPADE (with default parameters, see text) which can be found here: http://pengqiu.gatech.edu/software/SPADE/
The data are available through the following flowrepository link