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The use of SSMD-based false discovery and false nondiscovery rates in genome-scale RNAi screens
Zhang X.D.; Lacson R.; Yang R.; Marine S.D.; McCampbell A.; Toolan D.M.; Hare T.R.; Kajdas J.; Berger J.P.; Holder D.J.; Heyse J.F.; Ferrer M.
2010-10-01
Source PublicationJournal of Biomolecular Screening
ISSN10870571 1552454X
Volume15Issue:9Pages:1123-1131
AbstractIn genome-scale RNA interference (RNAi) screens, it is critical to control false positives and false negatives statistically. Traditional statistical methods for controlling false discovery and false nondiscovery rates are inappropriate for hit selection in RNAi screens because the major goal in RNAi screens is to control both the proportion of short interfering RNAs (siR-NAs) with a small effect among selected hits and the proportion of siRNAs with a large effect among declared nonhits. An effective method based on strictly standardized mean difference (SSMD) has been proposed for statistically controlling false discovery rate (FDR) and false nondiscovery rate (FNDR) appropriate for RNAi screens. In this article, the authors explore the utility of the SSMD-based method for hit selection in RNAi screens. As demonstrated in 2 genome-scale RNAi screens, the SSMD-based method addresses the unmet need of controlling for the proportion of siRNAs with a small effect among selected hits, as well as controlling for the proportion of siRNAs with a large effect among declared nonhits. Furthermore, the SSMD-based method results in reasonably low FDR and FNDR for selecting inhibition or activation hits. This method works effectively and should have a broad utility for hit selection in RNAi screens with replicates. © 2010 Society for Laboratory Automation and Screening.
Keyword-value false discovery rate false nondiscovery rate high-throughput screening p q RNAi
DOI10.1177/1087057110381919
URLView the original
Language英語
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Cited Times [WOS]:15   [WOS Record]     [Related Records in WOS]
Document TypeJournal article
CollectionFaculty of Health Sciences
AffiliationMerck Research Laboratories
Recommended Citation
GB/T 7714
Zhang X.D.,Lacson R.,Yang R.,et al. The use of SSMD-based false discovery and false nondiscovery rates in genome-scale RNAi screens[J]. Journal of Biomolecular Screening,2010,15(9):1123-1131.
APA Zhang X.D..,Lacson R..,Yang R..,Marine S.D..,McCampbell A..,...&Ferrer M..(2010).The use of SSMD-based false discovery and false nondiscovery rates in genome-scale RNAi screens.Journal of Biomolecular Screening,15(9),1123-1131.
MLA Zhang X.D.,et al."The use of SSMD-based false discovery and false nondiscovery rates in genome-scale RNAi screens".Journal of Biomolecular Screening 15.9(2010):1123-1131.
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