When and why are principal component scores a good tool for visualizing high-dimensional data?

Abstract: Principal component analysis (PCA) is a popular dimension reduction technique often used to visualize high-dimensional data structures. In genomics, this can involve millions of variables, but only tens to hundreds of observations. Theoretically, such extreme high-dimensionality will cause biased or inconsistent eigenvector estimates, but in practice the principal component scores are used for visualization with great success. In this paper, we explore when and why the classical principal component scores can be used to visualize structures in high-dimensional data, even when there are few observations compared to the number of variables. Our argument is two-fold: First, we argue that eigenvectors related to pervasive signals will have eigenvalues scaling linearly with the number of variables. Second, we prove that for linearly increasing eigenvalues, the sample component scores will be scaled and rotated versions of the population scores, asymptotically. Thus the visual information of the sample scores will be unchanged, even though the sample eigenvectors are biased. In the case of pervasive signals, the principal component scores can be used to visualize the population structures, even in extreme high-dimensional situations.