Detecting outlier samples in microarray data.
In this paper, we address the problem of detecting outlier samples with highly different expression patterns in microarray data. Although outliers are not common, they appear even in widely used benchmark data sets and can negatively affect microarray data analysis. It is important to identify outliers in order to explore underlying experimental or biological problems and remove erroneous data. We propose an outlier detection method based on principal component analysis (PCA) and robust estimation of Mahalanobis distances that is fully automatic. We demonstrate that our outlier detection method identifies biologically significant outliers with high accuracy and that outlier removal improves the prediction accuracy of classifiers. Our outlier detection method is closely related to existing robust PCA methods, so we compare our outlier detection method to a prominent robust PCA method.
Shieh
Albert D
AD
Harvard University. shieh@fas.harvard.edu
Hung
Yeung Sam
YS
D003110:Colonic Neoplasms / Q000175:diagnosis / Q000235:genetics; D030541:Databases, Genetic; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data*; D016311:Outliers, DRG / Q000706:statistics & numerical data*; D025341:Principal Component Analysis