Power and Stability Properties of Resampling-based Multiple Testing Procedures with Applications to Gene Oncology Studies

Overview

Journal Comput Math Methods Med

Publisher Hindawi

Specialty Medical Informatics

Date 2013 Dec 19

PMID 24348741

Citations 8

Authors

Dongmei Li

Timothy D Dye

Affiliations

Soon will be listed here.

Abstract

Resampling-based multiple testing procedures are widely used in genomic studies to identify differentially expressed genes and to conduct genome-wide association studies. However, the power and stability properties of these popular resampling-based multiple testing procedures have not been extensively evaluated. Our study focuses on investigating the power and stability of seven resampling-based multiple testing procedures frequently used in high-throughput data analysis for small sample size data through simulations and gene oncology examples. The bootstrap single-step minP procedure and the bootstrap step-down minP procedure perform the best among all tested procedures, when sample size is as small as 3 in each group and either familywise error rate or false discovery rate control is desired. When sample size increases to 12 and false discovery rate control is desired, the permutation maxT procedure and the permutation minP procedure perform best. Our results provide guidance for high-throughput data analysis when sample size is small.

Citing Articles

Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed.

Lin A, Ma J, Xu F, Xu W, Jiang H, Zhang H Plants (Basel). 2020; 9(8).

PMID: 32752101 PMC: 7465011. DOI: 10.3390/plants9080977.

Methods to adjust for multiple comparisons in the analysis and sample size calculation of randomised controlled trials with multiple primary outcomes.

Vickerstaff V, Omar R, Ambler G BMC Med Res Methodol. 2019; 19(1):129.

PMID: 31226934 PMC: 6588937. DOI: 10.1186/s12874-019-0754-4.

Infected with .

Ma J, Wei L, Lin A, Zhang C, Sun W, Yang B Genes (Basel). 2019; 10(4).

PMID: 30979089 PMC: 6523698. DOI: 10.3390/genes10040296.

Weighted gene co‑expression network analysis for identifying hub genes in association with prognosis in Wilms tumor.

Wang X, Song P, Huang C, Yuan N, Zhao X, Xu C Mol Med Rep. 2019; 19(3):2041-2050.

PMID: 30664180 PMC: 6390024. DOI: 10.3892/mmr.2019.9881.

Familiarity with social sounds alters c-Fos expression in auditory cortex and interacts with estradiol in locus coeruleus.

Moreno A, Gumaste A, Adams G, Chong K, Nguyen M, Shepard K Hear Res. 2018; 366:38-49.

PMID: 29983289 PMC: 6470399. DOI: 10.1016/j.heares.2018.06.020.

References

Mei R, Galipeau P, Prass C, Berno A, Ghandour G, Patil N . Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res. 2000; 10(8):1126-37. PMC: 2235196. DOI: 10.1101/gr.10.8.1126. View

Edgar R, Domrachev M, Lash A . Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res. 2001; 30(1):207-10. PMC: 99122. DOI: 10.1093/nar/30.1.207. View

Kulesh D, Clive D, Zarlenga D, GREENE J . Identification of interferon-modulated proliferation-related cDNA sequences. Proc Natl Acad Sci U S A. 1987; 84(23):8453-7. PMC: 299562. DOI: 10.1073/pnas.84.23.8453. View

Rubin D, Dudoit S, van der Laan M . A method to increase the power of multiple testing procedures through sample splitting. Stat Appl Genet Mol Biol. 2006; 5:Article19. DOI: 10.2202/1544-6115.1148. View

Buck M, Lieb J . ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics. 2004; 83(3):349-60. DOI: 10.1016/j.ygeno.2003.11.004. View

Tusher V, Tibshirani R, Chu G . Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A. 2001; 98(9):5116-21. PMC: 33173. DOI: 10.1073/pnas.091062498. View

Jemal A, Siegel R, Ward E, Murray T, Xu J, Smigal C . Cancer statistics, 2006. CA Cancer J Clin. 2006; 56(2):106-30. DOI: 10.3322/canjclin.56.2.106. View

Pollack J, Perou C, Alizadeh A, Eisen M, Pergamenschikov A, Williams C . Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet. 1999; 23(1):41-6. DOI: 10.1038/12640. View

Moreno C, Matyunina L, Dickerson E, Schubert N, Bowen N, Logani S . Evidence that p53-mediated cell-cycle-arrest inhibits chemotherapeutic treatment of ovarian carcinomas. PLoS One. 2007; 2(5):e441. PMC: 1859837. DOI: 10.1371/journal.pone.0000441. View

10.

Lashkari D, DeRisi J, McCusker J, Namath A, Gentile C, Hwang S . Yeast microarrays for genome wide parallel genetic and gene expression analysis. Proc Natl Acad Sci U S A. 1997; 94(24):13057-62. PMC: 24262. DOI: 10.1073/pnas.94.24.13057. View

11.

Hehir-Kwa J, Egmont-Petersen M, Janssen I, Smeets D, Geurts van Kessel A, Veltman J . Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis. DNA Res. 2007; 14(1):1-11. PMC: 2779891. DOI: 10.1093/dnares/dsm002. View

12.

Schena M, Shalon D, Davis R, Brown P . Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995; 270(5235):467-70. DOI: 10.1126/science.270.5235.467. View