The DOI matches its Crossref record; 108 of the 108 references it cites were found in a registry or an index.
Multiple hypothesis testing in genomics
Abstract
This paper presents an overview of the current state of the art in multiple testing in genomics data from a user's perspective. We describe methods for familywise error control, false discovery rate control and false discovery proportion estimation and confidence, both conceptually and practically, and explain when to use which type of error rate. We elaborate on the assumptions underlying the methods and discuss pitfalls in the interpretation of results. In our discussion, we take into account the exploratory nature of genomics experiments, looking at selection of genes before or after testing, and at the role of validation experiments.
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Citations
Cites
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A Simple Sequentially Rejective Multiple Test Procedure
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Significance analysis of microarrays applied to the ionizing radiation response
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The control of the false discovery rate in multiple testing under dependency
Benjamini, Y., & Yekutieli, D. (2001) · The Annals of Statistics · doi:10.1214/aos/1013699998 · Cited by 10,490
A Gene-Expression Signature as a Predictor of Survival in Breast Cancer
van de Vijver, M. J., He, Y. D., van 't Veer, L. J., Dai, H., Hart, A. A. M., Voskuil, D. W., Schreiber, G. J., Peterse, J. L., Roberts, C., Marton, M. J., et al. (2002) · New England Journal of Medicine · doi:10.1056/nejmoa021967 · Cited by 6,488
No adjustments are needed for multiple comparisons.
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What's wrong with Bonferroni adjustments
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A Direct Approach to False Discovery Rates
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GOATOOLS: A Python library for Gene Ontology analyses
Klopfenstein, D. V., Zhang, L., Pedersen, B. S., Ramírez, F., Warwick Vesztrocy, A., Naldi, A., Mungall, C. J., Yunes, J. M., Botvinnik, O., Weigel, M., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-28948-z · Cited by 1,290
Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability
Lelieveld, S. H., Reijnders, M. R. F., Pfundt, R., Yntema, H. G., Kamsteeg, E.-J., de Vries, P., de Vries, B. B. A., Willemsen, M. H., Kleefstra, T., Löhner, K., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4352 · Cited by 442
A practical guide to methods controlling false discoveries in computational biology
Korthauer, K., Kimes, P. K., Duvallet, C., Reyes, A., Subramanian, A., Teng, M., Shukla, C., Alm, E. J., & Hicks, S. C. (2019) · Genome Biology · doi:10.1186/s13059-019-1716-1 · Cited by 436
Rubin, M. (2021) · Synthese · doi:10.1007/s11229-021-03276-4 · Cited by 371
Truhn, D., Schrading, S., Haarburger, C., Schneider, H., Merhof, D., & Kuhl, C. (2019) · Radiology · doi:10.1148/radiol.2018181352 · Cited by 273
When Null Hypothesis Significance Testing Is Unsuitable for Research: A Reassessment
Szucs, D., & Ioannidis, J. P. A. (2017) · Frontiers in Human Neuroscience · doi:10.3389/fnhum.2017.00390 · Cited by 298
MultipleTesting.com: A tool for life science researchers for multiple hypothesis testing correction
Menyhart, O., Weltz, B., & Győrffy, B. (2021) · PLOS ONE · doi:10.1371/journal.pone.0245824 · Cited by 216
Design choices for observational studies of the effect of exposure on disease incidence
Gail, M. H., Altman, D. G., Cadarette, S. M., Collins, G., Evans, S. J., Sekula, P., Williamson, E., & Woodward, M. (2019) · BMJ Open · doi:10.1136/bmjopen-2019-031031 · Cited by 36
Genetic Variants and Early Cigarette Smoking and Nicotine Dependence Phenotypes in Adolescents
O'Loughlin, J., Sylvestre, M.-P., Labbe, A., Low, N. C., Roy-Gagnon, M.-H., Dugas, E. N., Karp, I., & Engert, J. C. (2014) · PLoS ONE · doi:10.1371/journal.pone.0115716 · Cited by 21
The socioeconomic landscape of the exposome during pregnancy
Sum, K. K., Tint, M. T., Aguilera, R., Dickens, B. S. L., Choo, S., Ang, L. T., Phua, D., Law, E. C., Ng, S., Tan, K. M.-L., et al. (2022) · Environment International · doi:10.1016/j.envint.2022.107205 · Cited by 18
Burger, T. (2023) · PROTEOMICS · doi:10.1002/pmic.202200406 · Cited by 10
“” In other words, the MTC can either be an FWER with statistical guarantees (Holm’s method amounts to a sequential Bonferroni-like control of the FWER [27]), or an FDR, without statistical guarantees (BH refers to Benjamini and Hochberg procedure to control the FDR [18]).”
Method
Metadata
- Authors
- Goeman, J. J., & Solari, A.
- Venue
- Statistics in Medicine
- Publisher
- Wiley
- Published
- 2014-01-08
- Volume
- 33
- Issue
- 11
- Pages
- 1946-1978
- ISSN
- 0277-6715 (ISSN-L)
- OpenAlex
- W2099657218
- Cited by
- 375
- References
- 108
- FWCI
- 24.40
- Type
- journal article
- Language
- en
- Open access
- closed
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