RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Export

@article{citeulike:1033144, abstract = {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 http://www.bioconductor.org. A web-based interface will soon be available at http://cactus.salk.edu/RankProd}, address = {Plant Biology Laboratory La Jolla, CA, USA. fhong@salk.edu}, author = {Hong, F. and Breitling, R. and McEntee, C. W. and Wittner, B. S. and Nemhauser, J. L. and Chory, J.}, citeulike-article-id = {1033144}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/16982708}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=16982708}, day = {15}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {affymetrix, bioconductor, microarray, software}, month = {November}, number = {22}, pages = {2825--2827}, posted-at = {2007-11-13 21:43:39}, priority = {3}, title = {RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/16982708}, volume = {22}, year = {2006} }

TY - JOUR ID - citeulike:1033144 L3 - citeulike-article-id:1033144 N2 - 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 http://www.bioconductor.org. A web-based interface will soon be available at http://cactus.salk.edu/RankProd IS - 22 JF - Bioinformatics SN - 1460-2059 AD - Plant Biology Laboratory La Jolla, CA, USA. fhong@salk.edu EP - 2827 TI - RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. VL - 22 SP - 2825 KW - affymetrix KW - bioconductor KW - microarray KW - software AU - Hong, F AU - Breitling, R AU - McEntee, CW AU - Wittner, BS AU - Nemhauser, JL AU - Chory, J PY - 2006/11/15/ UR - http://view.ncbi.nlm.nih.gov/pubmed/16982708 ER -