twilight.getlambda(xin, verbose = TRUE)
xin
. The final estimate is chosen based upon a Wilcoxon test comparison between objective function values of $\lambda=0$ and each $\lambda>0$. The penalized objective function should not differ a lot from the unpenalized one. Therefore, the highest lambda that leads to a non-significant difference in means is chosen.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.
twilight