||twilight is an R/Bioconductor package that includes several functions for the statistical analysis of two-condition microarray data. The main algorithm for estimating the local false discovery rate is described in Scheid and Spang (2004a). The newer versions of twilight include the permutation filtering algorithm introduced in Scheid and Spang (2006).
Scheid S and Spang R (2006):
Permutation filtering: A novel concept for significance analysis of large-scale genomic data
In: Apostolico A, Guerra C, Istrail S, Pevzner P, and Waterman M (Eds.): Research in Computational Molecular Biology: 10th Annual International Conference, Proceedings of RECOMB 2006, Venice, Italy, April 2-5, 2006.
Lecture Notes in Computer Science vol. 3909, Springer, Heidelberg, pp. 338-347.
ISSN: 0302-9743, ISBN: 3-540-33295-2.
[ pdf | doi:10.1007/11732990_29 ]
Scheid S and Spang R (2004a):
A stochastic downhill search algorithm for estimating the local false discovery rate
IEEE Transactions on Computational Biology and Bioinformatics 1(3):98-108.
[ abstract | pdf | notice]
Scheid S and Spang R (2004b):
Estimation of Local False Discovery Rates - User's Guide to the Bioconductor Package TWILIGHT
CompDiag Technical Report Nr. 2004/01 Nov. 2004
[ pdf ]
For further information please visit the compdiag projects Local False Discovery Rate or Permutation Filtering.
Download the tared and gzipped source file as submitted to Bioconductor. To run the package, you need R or higher and the R packages splines and stats. Package twilight includes a user's manual which can be downloaded separately from above.
Direct installation from the CompDiag R-repository
Start the R version where you want to install TWILIGHT. Use the following commands on the R prompt to install TWILIGHT directly from our repository:
z <- getReposEntry("http://compdiag.molgen.mpg.de/software/Rrepos")
For commercial use of TWILIGHT, please visit the webpage of the NGFN Technology Transfer Center on genome-marketplace.
[ pdf ]