twilight.pval
on leukemia data set of Golub et al. (1999), as given in data(Golub_Merge)
in library(golubEsets)
.First step was the variance-stabilizing normalization of Huber et al. (2002) in library(vsn)
: golubNorm <- justvsn(Golub_Merge)
.
The function call was then expval <- twilight.pval(golubNorm,id)
with id <- as.numeric(Golub_Merge$ALL.AML)
.
data(expval)
Huber W, von Heydebreck A, Sultmann H, Poustka A and Vingron M (2002): Variance stabilization applied to microarray data calibration and to the quantification of differential expression, Bioinformatics 18, suppl. 1, S96--S104.
Scheid S and Spang R (2004): A stochastic downhill search algorithm for estimating the local false discovery rate, IEEE TCBB 1(3), 98--108.
Scheid S and Spang R (2005): twilight; a Bioconductor package for estimating the local false discovery rate, Bioinformatics 21(12), 2921--2922.
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.
Tusher VG, Tibshirani R and Chu G (2001): Significance analysis of mircroarrays applied to the ionizing response, PNAS 98(9), 5116--5121.