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Bioinformatics Advance Access published online on April 7, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti436
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received January 31, 2005
Revised April 5, 2005
Accepted April 5, 2005

Applications note

TWILIGHT - a Bioconductor package for estimating the local false discovery rate

Stefanie Scheid 1* and Rainer Spang 1

1 Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Ihnestrasse 63-73, D-14195 Berlin, Germany

* To whom correspondence should be addressed.
Stefanie Scheid, E-mail: stefanie.scheid{at}molgen.mpg.de


  Abstract

Summary: TWILIGHT is a Bioconductor compatible package for analysing the statistical significance of differentially expressed genes. It is based on the concept of the local false discovery rate, a generalization of the frequently used global FDR. TWILIGHT implements the heuristic search algorithm for estimating the local FDR introduced in Scheid and Spang (2004). In addition to the raw significance measures, it produces diagnostic plots, which provide insight into the extent of differential expression across genes.

Availability: http://www.bioconductor.org.

Supplementary information: Please visit our software webpage on http://compdiag.molgen.mpg.de/software.


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