The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Testing significance relative to a fold-change threshold is a TREAT
Open accessAbstract
Motivation: Statistical methods are used to test for the differential expression of genes in microarray experiments. The most widely used methods successfully test whether the true differential expression is different from zero, but give no assurance that the differences found are large enough to be biologically meaningful. Results: We present a method, t-tests relative to a threshold (TREAT), that allows researchers to test formally the hypothesis (with associated p-values) that the differential expression in a microarray experiment is greater than a given (biologically meaningful) threshold. We have evaluated the method using simulated data, a dataset from a quality control experiment for microarrays and data from a biological experiment investigating histone deacetylase inhibitors. When the magnitude of differential expression is taken into account, TREAT improves upon the false discovery rate of existing methods and identifies more biologically relevant genes. Availability: R code implementing our methods is contributed to the software package limma available at http://www.bioconductor.org. Contact: smyth@wehi.edu.au
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Cites
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482
Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829
Self-citationDAVID: Database for Annotation, Visualization, and Integrated Discovery
Dennis, G., Sherman, B. T., Hosack, D. A., Yang, J., Gao, W., Lane, H. C., & Lempicki, R. A. (2003) · Genome Biology · doi:10.1186/gb-2003-4-5-p3 · Cited by 9,327
limma: Linear Models for Microarray Data
Smyth, G. K. (2005) · Statistics for Biology and Health · doi:10.1007/0-387-29362-0_23 · Cited by 5,796
Self-citationCox, D. R., & Hinkley, D. V. (1974) · doi:10.1007/978-1-4899-2887-0 · Cited by 3,089
Empirical array quality weights in the analysis of microarray data
Ritchie, M. E., Diyagama, D., Neilson, J., van Laar, R., Dobrovic, A., Holloway, A., & Smyth, G. K. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-261 · Cited by 312
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Cited by
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
limma powers differential expression analyses for RNA-sequencing and microarray studies
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv007 · Cited by 40,458
Self-citationPooling across cells to normalize single-cell RNA sequencing data with many zero counts
L. Lun, A. T., Bach, K., & Marioni, J. C. (2016) · Genome Biology · doi:10.1186/s13059-016-0947-7 · Cited by 1,108
Evaluation of variability in human kidney organoids
Phipson, B., Er, P. X., Combes, A. N., Forbes, T. A., Howden, S. E., Zappia, L., Yen, H.-J., Lawlor, K. T., Hale, L. J., Sun, J., et al. (2019) · Nature Methods · doi:10.1038/s41592-018-0253-2 · Cited by 253
Complementarity and redundancy of IL-22-producing innate lymphoid cells
Rankin, L. C., Girard-Madoux, M. J. H., Seillet, C., Mielke, L. A., Kerdiles, Y., Fenis, A., Wieduwild, E., Putoczki, T., Mondot, S., Lantz, O., et al. (2016) · Nature Immunology · doi:10.1038/ni.3332 · Cited by 249
“A linear model was fitted to each gene 49 and empirical Bayes moderated t-statistics were used to assess differences in expression 50 .”
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Metadata
- Authors
- McCarthy, D. J., & Smyth, G. K.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-01-28
- Volume
- 25
- Issue
- 6
- Pages
- 765-771
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2126398084
- Cited by
- 721
- References
- 6
- FWCI
- 6.96
- Type
- journal article
- Language
- en
- Open access
- hybrid
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