Error Rates and Powers in Genome-Scale RNAi Screens

Abstract

For hit selection in genome-scale RNAi research, we do not want to miss small interfering RNAs (siRNAs) with large effects; meanwhile, we do not want to include siRNAs with small or no effects in the list of selected hits. There is a strong need to control both the false-negative rate (FNR), in which the siRNAs with large effects are not selected as hits, and the restricted false-positive rate (RFPR), in which the siRNAs with no or small effects are selected as hits. An error control method based on strictly standardized mean difference (SSMD) has been proposed to maintain a flexible and balanced control of FNR and RFPR. In this article, the authors illustrate how to maintain a balanced control of both FNR and RFPR using the plot of error rate versus SSMD as well as how to keep high powers using the plot of power versus SSMD in RNAi high-throughput screening experiments. There are relationships among FNR, RFPR, Type I and II errors, and power. Understanding the differences and links among these concepts is essential for people to use statistical terminology correctly and effectively for data analysis in genome-scale RNAi screens. Here the authors explore these differences and links. (Journal of Biomolecular Screening 2009:230-238)

Keywords

restricted false-positive rate false-negative rate strictly standardized mean difference Type I error Type II error power

References

Fire A. , Xu SQ , Montgomery MK , Kostas SA , Driver SE , Mello CC : Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 1998;391:806-811.

Hannon GJ , Zamore PD : Small RNAs, big biology: biochemical studies of RNA interference. In Hannon GJ (ed): A Guide to Gene Silencing. New York: Cold Spring Harbor Laboratory Press; 2003:87-108.

Napoli C. , Lemieux C. , Jorgensen R. : Introduction of a chimeric chalcone synthase gene into petunia results in reversible co-suppression of homologous genes in trans. Plant Cell 1990;2:279-289.

Zhang XHD : A pair of new statistical parameters for quality control in RNA interference high-throughput screening assays. Genomics 2007;89:552-561.

Zhang XHD , Espeseth AS , Johnson EN , Chin J. , Gates A. , Mitnaul LJ , et al: Integrating experimental and analytic approaches to improve data quality in genome-wide RNAi screens. J Biomol Screen 2008;13:378-389.

Zhang XHD : Novel analytic criteria and effective plate designs for quality control in genome-wide RNAi screens. J Biomol Screen 2008;13:363-377.

Wiles AM , Ravi D. , Bhavani S. , Bishop AJR : An analysis of normalization methods for Drosophila RNAi genomic screens and development of a robust validation scheme. J Biomol Screen 2008;13:777-784.

Zhang XHD : A new method with flexible and balanced control of false negatives and false positives for hit selection in RNA interference high-throughput screening assays. J Biomol Screen 2007;12:645-655.

Zhang XHD , Ferrer M. , Espeseth AS , Marine SD , Stec EM , Crackower MA , et al: The use of strictly standardized mean difference for hit selection in primary RNA interference high-throughput screening experiments. J Biomol Screen 2007;12:497-509.

10.

Zhang XHD : Genome-wide screens for effective siRNAs through assessing the size of siRNA effects. BMC Res Notes 2008;1:33.

11.

Zhao HF , L'Abbe D. , Jolicoeur N. , Wu MQ , Li Z. , Yu ZB , et al: High-throughput screening of effective siRNAs from RNAi libraries delivered via bacterial invasion. Nat Methods 2005;2:967-973.

12.

Schechtman E. : A method with flexible and balanced control of false negatives and false positives for hit selection in RNA interference high-throughput screening assays: a statistical terminology. J Biomol Screen 2008;13:309-311.

13.

Ripley BD : Pattern Recognition and Neural Networks. New York : Cambridge University Press, 1996 .

14.

Hedges LV , Olkin I. : Statistical Methods for Meta-Analysis. San Diego : Academic Press, 1985.

15.

Zhang XHD : A method effectively comparing gene effects in multiple conditions in RNAi and expression profiling research. Pharmacogenomics. In press.

16.

Chung NJ , Zhang XD , Kreamer A. , Locco L. , Kuan PF , Bartz S. , et al: Median absolute deviation to improve hit selection for genome-scale RNAi screens. J Biomol Screen 2008;13:149-158.

17.

Malo N. , Hanley JA , Cerquozzi S. , Pelletier J. , Nadon R. : Statistical practice in high-throughput screening data analysis. Nat Biotechnol 2006;24:167-175.

18.

Zhang XHD , Yang XC , Chung NJ , Gates A. , Stec E. , Kunapuli P. , et al: Robust statistical methods for hit selection in RNA interference high-throughput screening experiments. Pharmacogenomics 2006;7: 299-309.

19.

Zhang XHD , Kuan PF , Ferrer M. , Shu XH , Liu YCX , Gates AT , et al: Hit selection with false discovery rate control in genome-scale RNAi screens. Nucleic Acids Res 2008;36:4667-4679.

20.

Zhou H. , Xu M. , Huang Q. , Gates AT , Zhang XHD , Stec E. , et al: Genome-scale RNAi screen for host factors required for HIV replication . Cell Host Microbe 2008;4:495-504.

21.

Tamhane AC , Dunlop DD : Statistics and Data Analysis. Upper Saddle River, NJ: Prentice Hall, 2000.