I am interested in using SciClone for tumor heterogeneity analysis, and was testing out my ability to properly run it by recreating Figs 3 and 5 from Miller and White et al. 2014 using the data and scripts available at github.com/genome/sciclone-meta. While my recreation of Fig. 5 appears identical to that published, my analysis (please see image below) of the data available for Fig. 3 using the provided run.R script differs from that in the publication, in that I am getting an extra and quite small cluster (Cluster 2 in image below). Has anyone else noticed this, and do you know what might be causing it?