179
Views
0
CrossRef citations to date
0
Altmetric
Original Articles

Evaluation of false discovery rate and power via sample size in microarray studies

, &
Pages 489-500 | Received 24 Jul 2010, Accepted 08 Jun 2011, Published online: 25 Jul 2011

References

  • Barabasi , A.-L. and Oltvai , Z. N. 2004 . Network biology: Understanding the cell's functional organization . Nat. Rev. Genet. , 5 : 101 – 113 .
  • Benjamini , Y. and Hochberg , Y. 1995 . Controlling the false discovery rate: A practical and powerful approach to multiple testing . J. Roy. Statist. Soc. B , 57 : 289 – 300 .
  • Dudoit , S. , Yang , Y. H. and Callow , M. J. 2002 . Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments . Statist. Sinica , 12 : 111 – 139 .
  • Efron , B. 2004 . Large-scale simultaneous hypothesis testing: The choice of a null hypothesis . J. Amer. Statist. Assoc. , 99 : 96 – 104 .
  • Efron , B. , Tibshirani , R. and Storey , J. D. 2001 . Empirical Bayes analysis of a microarray experiment . J. Amer. Statist. Assoc. , 96 : 1151 – 1160 .
  • Farcomeni , A. 2008 . A review of modern multiple hypothesis testing, with particular attention to the false discovery proportion . Statist. Methods Med. Res. , 17 : 347 – 388 .
  • Ferreira , J. A. and Zwinderman , A. 2006 . Approximate sample size calculations with microarray data: An illustration . Statist. Appl. Genet. Mol. Biol. , 5 : 17
  • Hu , J. H. , Zou , F. and Wright , F. A. 2005 . Practical FDR-based sample size calculations in microarray experiments . Bioinformatics , 21 : 3264 – 3272 .
  • van Iterson , M. , 't Hoen , P. and Pedotti , P. 2009 . Relative power and sample size analysis on gene expression profiling data . BMC Genom. , 10 : 439
  • Jung , S. H. 2005 . Sample size for FDR-control in microarray data analysis . Bioinformatics , 21 : 3097 – 3104 .
  • Lee , M. L.T. , Kuo , F. C. and Whitmore , G. A. 2000 . Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations . Proc. Natl. Acad. Sci. USA , 97 : 9834 – 9839 .
  • Li , S. Y.S. , Bigler , J. and Lampe , J. W. 2005 . FDR-controlling testing procedures and sample size determination for microarrays . Statist. Med. , 24 : 2267 – 2280 .
  • Lin , C. S. and Hsu , C. W. 2005 . Differentially transcribed genes in skeletal muscle of Duroc and Taoyuan pigs . J. Anim. Sci. , 83 : 2075 – 2086 .
  • Liu , P. and Hwang , J. T.G. 2007 . Quick calculation for sample size while controlling false discovery rate with application to microarray analysis . Bioinformatics , 23 : 739 – 746 .
  • Mclachlan , G. J. , Bean , R. W. and Jones , L. B.T. 2006 . A simple implementation of a normal mixture approach to differential gene expression in multiclass microarrays . Bioinformatics , 22 : 1608 – 1615 .
  • O'rourke , J. A. , Charlson , D. V. and Gonzalez , D. O. 2007 . Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines . BMC Genom. , 8 : 476
  • Pawitan , Y. , Michiels , S. and Koscielny , S. 2005 . False discovery rate, sensitivity and sample size for microarray studies . Bioinformatics , 21 : 3017 – 3024 .
  • Pounds , S. and Cheng , C. 2005 . Sample size determination for the false discovery rate . Bioinformatics , 21 : 4263 – 4271 .
  • Reverter , A. , Wang , Y. H. and Byrne , K. A. 2004 . Joint analysis of multiple cDNA microarray studies via multivariate mixed models applied to genetic improvement of beef cattle . J. Anim. Sci. , 82 : 3430 – 3439 .
  • Storey , J. D. 2003 . The positive false discovery rate: A Bayesian interpretation and the q-value . Ann. Statist. , 31 : 2013 – 2035 .
  • Storey , J. D. and Tibshirani , R. 2003 . Statistical significance for genomewide studies . Proc. Natl. Acad. Sci. USA , 100 : 9440 – 9445 .
  • Westfall , P. H. and Young , S. S. 1989 . P-value adjustments for multiple tests in multivariate binomial models . J. Amer. Statist. Assoc. , 84 : 780 – 786 .

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.