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How accurately can we control the FDR in analyzing microarray data?

Publication ,  Journal Article
Jung, S-H; Jang, W
Published in: Bioinformatics
July 15, 2006

We want to evaluate the performance of two FDR-based multiple testing procedures by Benjamini and Hochberg (1995, J. R. Stat. Soc. Ser. B, 57, 289-300) and Storey (2002, J. R. Stat. Soc. Ser. B, 64, 479-498) in analyzing real microarray data. These procedures commonly require independence or weak dependence of the test statistics. However, expression levels of different genes from each array are usually correlated due to coexpressing genes and various sources of errors from experiment-specific and subject-specific conditions that are not adjusted for in data analysis. Because of high dimensionality of microarray data, it is usually impossible to check whether the weak dependence condition is met for a given dataset or not. We propose to generate a large number of test statistics from a simulation model which has asymptotically (in terms of the number of arrays) the same correlation structure as the test statistics that will be calculated from the given data and to investigate how accurately the FDR-based testing procedures control the FDR on the simulated data. Our approach is to directly check the performance of these procedures for a given dataset, rather than to check the weak dependency requirement. We illustrate the proposed method with real microarray datasets, one where the clinical endpoint is disease group and another where it is survival.

Duke Scholars

Published In

Bioinformatics

DOI

EISSN

1367-4811

Publication Date

July 15, 2006

Volume

22

Issue

14

Start / End Page

1730 / 1736

Location

England

Related Subject Headings

  • Sensitivity and Specificity
  • Reproducibility of Results
  • Oligonucleotide Array Sequence Analysis
  • Models, Statistical
  • Models, Genetic
  • Gene Expression Profiling
  • Data Interpretation, Statistical
  • Bioinformatics
  • Algorithms
  • 49 Mathematical sciences
 

Citation

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MLA
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Jung, S.-H., & Jang, W. (2006). How accurately can we control the FDR in analyzing microarray data? Bioinformatics, 22(14), 1730–1736. https://doi.org/10.1093/bioinformatics/btl161
Jung, Sin-Ho, and Woncheol Jang. “How accurately can we control the FDR in analyzing microarray data?Bioinformatics 22, no. 14 (July 15, 2006): 1730–36. https://doi.org/10.1093/bioinformatics/btl161.
Jung S-H, Jang W. How accurately can we control the FDR in analyzing microarray data? Bioinformatics. 2006 Jul 15;22(14):1730–6.
Jung, Sin-Ho, and Woncheol Jang. “How accurately can we control the FDR in analyzing microarray data?Bioinformatics, vol. 22, no. 14, July 2006, pp. 1730–36. Pubmed, doi:10.1093/bioinformatics/btl161.
Jung S-H, Jang W. How accurately can we control the FDR in analyzing microarray data? Bioinformatics. 2006 Jul 15;22(14):1730–1736.

Published In

Bioinformatics

DOI

EISSN

1367-4811

Publication Date

July 15, 2006

Volume

22

Issue

14

Start / End Page

1730 / 1736

Location

England

Related Subject Headings

  • Sensitivity and Specificity
  • Reproducibility of Results
  • Oligonucleotide Array Sequence Analysis
  • Models, Statistical
  • Models, Genetic
  • Gene Expression Profiling
  • Data Interpretation, Statistical
  • Bioinformatics
  • Algorithms
  • 49 Mathematical sciences