Additional file 12.

A figure showing principal component analysis of matched adjacent normal tissues. (a) Scree plot showing the percent of data variation explained by the first 10 principal components of the patient matched adjacent normal tissue. The common reference design accounts for 84.58% of variations in gene expression observed in the data (Additional file 13), while principal components 2 and 3 are explained by variations in gene expression associated with tissue type, and components 4 through 8 are explained by variations in gene expression between individuals. (b) Scatter plot of principal component two against principal component 3. These two dimensions suffice to summarize the between tissue variation observed in the data, as demonstrated by the clustering of epithelial samples on the right of the plot (red), and stromal samples on the left (black). Analogously, in five dimensions, we can explain the variation between individuals. No other clinical characteristics were significantly associated with any principal components.

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Finak et al. Breast Cancer Research 2006 8:R58   doi:10.1186/bcr1608