Additional file 4: Figure S1.
Assessment of robustness of synovial gene expression heterogeneity. (A) Principal component analysis showing the first (x-axis) and second (y-axis) components of variation over approximately 7,000 probes and 49 patients using the prcomp R-function on quantile-normalized expression data. Each patient tissue is color-coded according to the groupings in Figure 1A, and grouping circles have been added for visual clarity. (B) Re-sampling analysis using partitioning around medoids (PAM) analysis of approximately 7,000 probes, 49 patients and 5 predefined clusters of tissue samples (k = 5). Heatmap colors represent the frequency with which a pair of samples are found in the same cluster, and are represented as a percentage of the total number of samplings in which the pair was observed. (C) Assessment of cluster robustness via determination of silhouette width of approximately 7,000 clustered probes from the 49 patients. Average silhouette widths for each of the five clusters are indicated.
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Dennis et al. Arthritis Research & Therapy 2014 16:R90 doi:10.1186/ar4555