Figure 2

Results for NJ and Parsimony analysis of normalized ratio data. These stacked histograms in this figure represent the SymD measures (symmetric distance away from the desired topology) for the Neighbor-Joining (Figures 2A and 2B) and parsimony (Figures 2C and 2D) CGH trees constructed from the ACUITY and Limma-based normalizations. Each stack represents the twelve iterations of the four different normalization procedures, detailed in Additional File 1: table S1. In histograms 2A and 2B, a correlation (COR) or a Euclidean distance matrix (EU) was calculated for each of the twelve iterations described using R and input into PAUP in order to construct NJ trees for the ALL, NEU, and CON taxa sets excluding (2A) and including (2B) the reference taxa, respectively. Figures 2C and 2D show stacked histograms for the corresponding Parsimony Majority Rule consensus (PMJ) trees binned with the GACK method. For each stack, the EPP threshold was varied in 10% increments from 0 to 100%. The same data is given in table form in Additional File 2: table S2.