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Biostatistics Advance Access originally published online on October 4, 2006
Biostatistics 2007 8(3):566-575; doi:10.1093/biostatistics/kxl029
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© The Author 2006. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org.

Cancer outlier differential gene expression detection

Baolin Wu

Division of Biostatistics, School of Public Health, University of Minnesota, A460 Mayo Building, MMC 303, Minneapolis, MN 55455, USA

baolin{at}biostat.umn.edu

We study statistical methods to detect cancer genes that are over- or down-expressed in some but not all samples in a disease group. This has proven useful in cancer studies where oncogenes are activated only in a small subset of samples. We propose the outlier robust t-statistic (ORT), which is intuitively motivated from the t-statistic, the most commonly used differential gene expression detection method. Using real and simulation studies, we compare the ORT to the recently proposed cancer outlier profile analysis (Tomlins and others, 2005) and the outlier sum statistic of Tibshirani and Hastie (2006). The proposed method often has more detection power and smaller false discovery rates. Supplementary information can be found at http://www.biostat.umn.edu/~baolin/research/ort.html.

Keywords: Cancer outlier profile analysis; Differential gene expression detection; Microarray; Robust; T-statistic

Received June 15, 2006; revised September 11, 2006; accepted for publication September 29, 2006.


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