Principal component analysis for clustering gene expression data

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ID: 296049
2001
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Abstract
Abstract Motivation: There is a great need to develop analytical methodology to analyze and to exploit the information contained in gene expression data. Because of the large number of genes and the complexity of biological networks, clustering is a useful exploratory technique for analysis of gene expression data. Other classical techniques, such as principal component analysis (PCA), have also been applied to analyze gene expression data. Using different data analysis techniques and different clustering algorithms to analyze the same data set can lead to very different conclusions. Our goal is to study the effectiveness of principal components (PCs) in capturing cluster structure. Specifically, using both real and synthetic gene expression data sets, we compared the quality of clusters obtained from the original data to the quality of clusters obtained after projecting onto subsets of the principal component axes. Results: Our empirical study showed that clustering with the PCs instead of the original variables does not necessarily improve, and often degrades, cluster quality. In particular, the first few PCs (which contain most of the variation in the data) do not necessarily capture most of the cluster structure. We also showed that clustering with PCs has different impact on different algorithms and different similarity metrics. Overall, we would not recommend PCA before clustering except in special circumstances. Contact: kayee@cs.washington.edu Supplementary information: http://www.cs.washington.edu/homes/kayee/pca * To whom correspondence should be addressed.
Reference Key
openalex_W2125310307 Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Ka Yee Yeung, Walter L. Ruzzo
Journal BMC Bioinformatics
Year 2001
DOI
10.1093/bioinformatics/17.9.763
URL
https://academic.oup.com/bioinformatics/article-pdf/17/9/763/539767/170763.pdf
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