1 / 1

Estimating Local False Discovery Rate in Gene Expression Studies

This paper discusses the estimation of the local false discovery rate (local FDR) in the context of two-sample designs and correlation tests for gene expression data. It provides insights into observed and expected scores, p- and q-values, and the overall percentage of differentially expressed genes. Diagnostic plots are presented to visualize expected versus observed scores, and the paper references a stochastic downhill search algorithm for local FDR estimation, along with a Bioconductor package called TWILIGHT for practical application.

rosalyn-britt
Télécharger la présentation

Estimating Local False Discovery Rate in Gene Expression Studies

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. 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.

More Related