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Normal Uniform Differential Gene Expression NUDGE

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Uses a simple univariate normal-uniform mixture model, in combination with new normalization methods for spread as well as mean that extend the lowess normalization. NUDGE is a simple method to find differentially expressed genes in cDNA microarrays. This method gives a high probability of differential expression to genes known/suspected a priori to be differentially expressed and a low probability to the others. In terms of known false positives and false negatives, NUDGE outperforms all multiple-replicate methods except for the Gamma-Gamma EBarrays method to which it offers comparable results with the added advantages of greater simplicity, speed, fewer assumptions and applicability to the single replicate case.

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NUDGE forum

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NUDGE classification

NUDGE specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
R
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS, Windows
License:
GNU General Public License version 2.0
Version:
1.40.0
Maintained:
Yes

NUDGE distribution

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NUDGE support

Documentation

Maintainer

  • Nema Dean <>

Credits

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Publications

Institution(s)

Department of Statistics, University of Washington, Seattle, WA, USA

Funding source(s)

This research was supported by NIH grant 8 R01 EB002137-02.

Link to literature

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