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Twilight: Estimating the local false discovery rate. Inference on two-sample designs and correlation tests for gene expression data: Observed and expected scores, p- and q-values (global FDR).

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twilight estimating the local false discovery rate
Twilight: Estimating the local false discovery rate
  • Inference on two-sample designs and correlation tests for gene expression data: Observed and expected scores, p- and q-values (global FDR).
  • Estimation of local FDR = probability that a gene is not differentially expressed at a certain u-value level (= p-value).
  • Estimation of overall percentage π0of differentially expressed genes.
  • Diagnostic plots: Expected vs. observed scores, q-values vs. size of gene list, volcano and local FDR plots (see Figure).
  • Combinatorial functions for complete enumeration of possible permutations.

References:

  • Scheid, S & Spang, R, A stochastic downhill search algorithm for estimating the local false discovery rate, IEEE Transactions on Computational Biology and Bioinformatics, vol. 1, p. 98-108, 2004.
  • Scheid, S & Spang, R, TWILIGHT - a Bioconductor package for estimating the local false discovery rate, to appear in Bioinformatics, 2005.