TWILIGHT 1.46.0 – Estimating the Local False Discovery Rate

TWILIGHT 1.46.0

:: DESCRIPTION

twilight is an R/Bioconductor package that includes several functions for the statistical analysis of two-condition microarray data.

::DEVELOPER

Institute of Functional Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux / MacOsX
  • R/Bioconductor

:: DOWNLOAD

 TWILIGHT

:: MORE INFORMATION

Citation

twilight; a Bioconductor package for estimating the local false discovery rate.
Scheid S, Spang R.
Bioinformatics. 2005 Jun 15;21(12):2921-2.

weighted_FDR 1.2 – Apply Weighted False Discovery Rate for Multiple Testing

weighted_FDR.R 1.2

:: DESCRIPTION

weighted_FDR.R is a Software to Apply Weighted False Discovery Rate for Multiple Testing. When testing a large number of hypotheses, such as an association genome scan, the power to detect modest effects can be low, due to the penalty for multiple testing.  This is especially true when traditional approaches such as the Bonferroni correction are employed.  The false discovery (FDR) approach increases power in a multiple testing scenario, but it is still challenging to obtain significant results when very large numbers of tests are performed. To enhance power further, a weighted FDR approach can be employed that involves weighting the hypotheses based on prior data, such as a linkage scan, knowledge about biological pathways, candidate genes and so on. The wFDR procedure up-weights likely candidates and down-weights others, while maintaining control of the overall rate of false discoveries. The weights must average to 1 and be chosen independently of the association test statistics.

::DEVELOPER

COMPUTATIONAL GENETICS LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 weighted_FDR.R

:: MORE INFORMATION

Citation:

Roeder K, Bacanu S-A, Wasserman L, Devlin B (2006)
Using linkage genome scans to improve power of association genome scans.
Am J Hum Genet. February 2006.