The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis
Open accessAbstract
Summary: While meta-analysis provides a powerful tool for analyzing microarray experiments by combining data from multiple studies, it presents unique computational challenges. The Bioconductor package RankProd provides a new and intuitive tool for this purpose in detecting differentially expressed genes under two experimental conditions. The package modifies and extends the rank product method proposed by Breitling et al., [(2004)FEBS Lett., 573, 83–92] to integrate multiple microarray studies from different laboratories and/or platforms. It offers several advantages over t-test based methods and accepts pre-processed expression datasets produced from a wide variety of platforms. The significance of the detection is assessed by a non-parametric permutation test, and the associated P-value and false discovery rate (FDR) are included in the output alongside the genes that are detected by user-defined criteria. A visualization plot is provided to view actual expression levels for each gene with estimated significance measurements. Availability: RankProd is available at Bioconductor . A web-based interface will soon be available at Contact: fhong@salk.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829
Multiple-laboratory comparison of microarray platforms
Irizarry, R. A., Warren, D., Spencer, F., Kim, I. F., Biswal, S., Frank, B. C., Gabrielson, E., Garcia, J. G. N., Geoghegan, J., Germino, G., et al. (2005) · Nature Methods · doi:10.1038/nmeth756 · Cited by 862
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Pearson, K. J., Baur, J. A., Lewis, K. N., Peshkin, L., Price, N. L., Labinskyy, N., Swindell, W. R., Kamara, D., Minor, R. K., Perez, E., et al. (2008) · Cell Metabolism · doi:10.1016/j.cmet.2008.06.011 · Cited by 1,162
mTORC1 controls the adaptive transition of quiescent stem cells from G0 to GAlert
Rodgers, J. T., King, K. Y., Brett, J. O., Cromie, M. J., Charville, G. W., Maguire, K. K., Brunson, C., Mastey, N., Liu, L., Tsai, C.-R., et al. (2014) · Nature · doi:10.1038/nature13255 · Cited by 776
Dai, Z., Coker, O. O., Nakatsu, G., Wu, W. K. K., Zhao, L., Chen, Z., Chan, F. K. L., Kristiansen, K., Sung, J. J. Y., Wong, S. H., et al. (2018) · Microbiome · doi:10.1186/s40168-018-0451-2 · Cited by 545
microRNA‐101 is a potent inhibitor of autophagy
Frankel, L. B., Wen, J., Lees, M., Høyer‐Hansen, M., Farkas, T., Krogh, A., Jäättelä, M., & Lund, A. H. (2011) · The EMBO Journal · doi:10.1038/emboj.2011.331 · Cited by 312
A re‐evaluation of fixed effect(s) meta‐analysis
Rice, K., Higgins, J. P. T., & Lumley, T. (2018) · Journal of the Royal Statistical Society Series A: Statistics in Society · doi:10.1111/rssa.12275 · Cited by 287
Metadata
- Authors
- Hong, F., Breitling, R., McEntee, C. W., Wittner, B. S., Nemhauser, J. L., & Chory, J.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-09-18
- Volume
- 22
- Issue
- 22
- Pages
- 2825-2827
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2172215633
- Cited by
- 752
- References
- 2
- FWCI
- 7.00
- Type
- journal article
- Language
- en
- Open access
- green
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