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Bioinformatics Advance Access published online on May 6, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti480
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received March 16, 2005
Revised April 20, 2005
Accepted April 28, 2005

Applications note

SDMinP: a program to control the family wise error rate using step-down minP adjusted p-values

M. Obreiter 1, C. Fischer 2, J. Chang-Claude 1, and L. Beckmann 1*

1 German Cancer Research Center DKFZ, Heidelberg, Germany
2 Institute of Human Genetics, University of Heidelberg, Germany

* To whom correspondence should be addressed.
L. Beckmann, E-mail: l.beckmann{at}dkfz.de


  Abstract

SDMinP is an easy-to-use program for fast calculation of empirical and adjusted p-values for correlated and uncorrelated hypotheses in multiple testing experiments. It is based on the Free Step-Down Resampling Method for controlling the Family Wise Error Rate, originally proposed by (Westfall and Young, 1993), and implements a variation of the efficient algorithm of Ge et al. (2003), who reduced the originally required re-sampling effort considerably and made the method computationally feasible. The program is independent of the underlying test statistic and works with provided observed and permutation test statistics.

Availability: http://www.dkfz.de/SDMinP.


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