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University of Michigan School of Public Health The University of Michigan Department of Biostatistics Working Paper Series Year Paper Shrunken p-values for assessing differential expression, with applications to genomic data analysis Debashis Ghosh * * University of Michigan, [email protected] This working paper is hosted by The Berkeley Electronic Press (bepress) and may not be commer- cially reproduced without the permission of the copyright holder. http://biostats.bepress.com/umichbiostat/paper55 Copyright c 2005 by the author.

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Page 1: University of Michigan School of Public Health · Shrunken p-values for assessing differential expression, with applications to genomic data analysis Debashis Ghosh Abstract n many

University of Michigan School of PublicHealth

The University of Michigan Department of Biostatistics WorkingPaper Series

Year Paper

Shrunken p-values for assessing differentialexpression, with applications to genomic data

analysis

Debashis Ghosh∗

∗University of Michigan, [email protected] working paper is hosted by The Berkeley Electronic Press (bepress) and may not be commer-cially reproduced without the permission of the copyright holder.

http://biostats.bepress.com/umichbiostat/paper55

Copyright c©2005 by the author.

Page 2: University of Michigan School of Public Health · Shrunken p-values for assessing differential expression, with applications to genomic data analysis Debashis Ghosh Abstract n many

Shrunken p-values for assessing differentialexpression, with applications to genomic data

analysis

Debashis Ghosh

Abstract

n many scientific problems involving high-throughput technology, inference mustbe made involving several hundreds or thousands of hypotheses. Recent atten-tion has focused on how to address the multiple testing issue; much focus hasbeen devoted towards use of the false discovery rate. In this article, we consideran alternative estimation procedure titled shrunken p-values for assessing differ-ential expression (SPADE). The estimators are motivated by risk considerationsfrom decision theory and lead to a completely new method for adjustment in themultiple testing problem. Some theoretical results are outlined. The proposedmethodology is illustrated using simulation studies and with application to datafrom a prostate cancer gene expression profiling study.

Page 3: University of Michigan School of Public Health · Shrunken p-values for assessing differential expression, with applications to genomic data analysis Debashis Ghosh Abstract n many

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Page 4: University of Michigan School of Public Health · Shrunken p-values for assessing differential expression, with applications to genomic data analysis Debashis Ghosh Abstract n many

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Page 24: University of Michigan School of Public Health · Shrunken p-values for assessing differential expression, with applications to genomic data analysis Debashis Ghosh Abstract n many

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http://biostats.bepress.com/umichbiostat/paper55