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Human Molecular Genetics, 2002, Vol. 11, No. 19 2223-2232
© 2002 Oxford University Press

Evaluating test statistics to select interesting genes in microarray experiments{dagger}

Charles Kooperberg1,*, Simonetta Sipione3, Michael LeBlanc1, Andrew D. Strand2, Elena Cattaneo3 and James M. Olson2

1Division of Public Health Sciences and 2Clinical Research Division, Fred Hutchinson Cancer Research Center, PO Box 19024, MP 1002, Seattle, WA 98109-1024, USA and 3University of Milan, Department of Pharmacological Sciences and Center of Excellence on Neurodegenerative Diseases, Italy

Received March 12, 2002; Accepted July 11, 2002

A randomization procedure to evaluate the significance level and the false-discovery rate in complex microarray experiments is proposed. A related graph can be used to compare different test statistics that can be used to analyze the same experiment. This graph is closely related to receiver operator characteristic (ROC) curves. The proposed method is applied to a subset of the data from a cell-line experiment related to Huntington's disease. A small simulation study compares the effectiveness of the proposed procedure with the significance analysis of microarrays (SAM) procedure.

* To whom correspondence should be addressed. Tel: +1 2066677808; Fax: +1 2066674142; Email: clk{at}fhcrc.org

{dagger} This paper is part of the Microarray Report Special Series. See Orr, H.J. (2002) Hum. Mol. Genet., 11: 1909–1910.


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