DOI: 10.1093/bioinformatics/btk013. Multidimensional local false discovery rate for microarray studies

Multidimensional local false discovery rate for microarray studies

10.1093/bioinformatics/btk013

Crossref journal-article

Oxford University Press (OUP)

Bioinformatics (286)

Abstract

AbstractMotivation: The false discovery rate (fdr) is a key tool for statistical assessment of differential expression (DE) in microarray studies. Overall control of the fdr alone, however, is not sufficient to address the problem of genes with small variance, which generally suffer from a disproportionally high rate of false positives. It is desirable to have an fdr-controlling procedure that automatically accounts for gene variability.Methods: We generalize the local fdr as a function of multiple statistics, combining a common test statistic for assessing DE with its standard error information. We use a non-parametric mixture model for DE and non-DE genes to describe the observed multi-dimensional statistics, and estimate the distribution for non-DE genes via the permutation method. We demonstrate this fdr2d approach for simulated and real microarray data.Results: The fdr2d allows objective assessment of DE as a function of gene variability. We also show that the fdr2d performs better than commonly used modified test statistics.Availability: An R-package OCplus containing functions for computing fdr2d() and other operating characteristics of microarray data is available atContact: alexander.ploner@meb.ki.se

Bibliography

Ploner, A., Calza, S., Gusnanto, A., & Pawitan, Y. (2005). Multidimensional local false discovery rate for microarray studies. Bioinformatics, 22(5), 556â565.

Authors 4

Alexander Ploner (first)
Stefano Calza (additional)
Arief Gusnanto (additional)
Yudi Pawitan (additional)

References 17 Referenced 65

10.1111/j.2517-6161.1995.tb02031.x / J. R. Statist. Soc. B / Controling the false discovery rate: a practical and powerful approach to multiple testing by Benjamini (1995)
10.1093/bioinformatics/bti063 / Bioinformatics / A simple procedure for estimating the false discovery rate by Dalmasso (2005)
10.1198/016214501753382129 / J. Am. Stat. Soc. / Empirical Bayes analysis of a microarray experiment by Efron (2001)
10.1056/NEJM200102223440801 / N. Engl. J. Med. / Gene-expression profiles in hereditary breast cancer by Hedenfalk (2001)
10.1007/978-1-4757-1923-9 / Testing statistical hypotheses by Lehmann (1986)
{'key': '2023012408530438800_b6', 'first-page': '31', 'article-title': 'Replicated microarray data', 'volume': '12', 'author': 'Lönnstedt', 'year': '2002', 'journal-title': 'Stat. Sinica'} / Stat. Sinica / Replicated microarray data by Lönnstedt (2002)
10.1093/biostatistics/5.2.155 / Biostatistics / Detecting differential gene expression with a semiparametric hierarchical mixture method by Newton (2004)
10.1093/oso/9780198507659.001.0001 / In All Likelihood: Statistical Modelling and Inference Using Likelihood by Pawitan (2001)
10.1093/bioinformatics/bti448 / Bioinformatics / False discovery rate, sensitivity and sample size for microarray studies by Pawitan (2005)
10.1093/bioinformatics/bti626 / Bioinformatics / Bias in the estimation of false discovery rate in microarray studies by Pawitan (2005)
10.1093/bioinformatics/btf877 / Bioinformatics / Identifying differentially expressed genes using false discovery rate controlling procedures by Reiner (2003)
10.1056/NEJMoa012914 / N. Engl. J. Med. / The use of molecular profiling to predict survival after chemotherapy for diffuse large-B-cell lymphoma by Rosenwald (2002)
10.2202/1544-6115.1027 / Stat. Appl. Genet. Mol. Biol. / Linear models and empirical Bayes methods for assessing differential expression in microarray experiments by Smyth (2004)
10.1073/pnas.1530509100 / Proc. Natl Acad. Sci. USA / Statistical significance for genomewide studies by Storey (2003)
10.1073/pnas.091062498 / Proc. Natl Acad. Sci. USA / Significance analysis of microarrays applied to the ionizing radiation response. [Erratum (2001) Proc. Natl Acad. Sci USA, 98, 10515.] by Tusher (2001)
10.1089/106652701753307520 / J. Comput. Biol. / Assessing gene significance from cDNA microarray expression data via mixed models by Wolfinger (2001)
10.1093/bioinformatics/bti108 / Bioinformatics / Identifying differentially expressed genes from microarray experiments via statistic synthesis by Yang (2005)

Dates

Type	When
Created	19 years, 8 months ago (Dec. 20, 2005, 9:18 p.m.)
Deposited	7 months, 2 weeks ago (Jan. 6, 2025, 12:30 p.m.)
Indexed	2 months ago (June 19, 2025, 10:44 p.m.)
Issued	19 years, 8 months ago (Dec. 20, 2005)
Published	19 years, 8 months ago (Dec. 20, 2005)
Published Online	19 years, 8 months ago (Dec. 20, 2005)
Published Print	19 years, 5 months ago (March 1, 2006)

Funders 0

None

BibTeX

@article{Ploner_2005, title={Multidimensional local false discovery rate for microarray studies}, volume={22}, ISSN={1367-4803}, url={http://dx.doi.org/10.1093/bioinformatics/btk013}, DOI={10.1093/bioinformatics/btk013}, number={5}, journal={Bioinformatics}, publisher={Oxford University Press (OUP)}, author={Ploner, Alexander and Calza, Stefano and Gusnanto, Arief and Pawitan, Yudi}, year={2005}, month=dec, pages={556–565} }

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