Principal component analysis and unsupervised hierarchical clustering of C&Ckines. (A) Plot of the first 2 PCs of the C&Ckine data. Normal samples (green) form a separate cluster, but MDS (blue) and AML (red) are indistinguishable. (B) Heatmap showing robustness of clustering in the presence of noise with SD = 1. For each of the 9 sample clusters, each sample clustered with almost all of its neighbors in the assigned cluster more than 50% of the time (and many samples did so > 80% of the time). Based on the silhouette width, more than 90% of samples were correctly clustered. Color bars along the y-axis show diagnosis (green represents normal; red, AML; and blue, MDS) and along the x-axis indicate the 9 highest branches in the dendogram. (C) Clustering of samples based on the dendogram in panel C. Unsupervised hierarchical clustering of C&Ckines based on the Pearson correlation of log intensity across samples using average linkage is shown by the dendogram across the top and left side. Results of a bootstrap cluster test of the reproducibility of hierarchical clustering of cytokines is shown with the color indicating the percentage of times that each pair of samples clustered together, with pure blue = 0% and pure yellow = 100%.