Dear List, Is there a lower limit for the number of tests you need to produce a moderated t-statistic with Limma? I am now analyzing a peptide array which after filtering has about 200 present spots. Can Limma be applied to borrow power over only 200 tests? Should it be applied to this situation? Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "School is an evil plot to suppress my individuality" Rose Friedman, age15

Hi Richard The lower limit for the number of tests you need to produce a moderated t-statistic with limma is 2. I would definitely recommend using limma to borrow power over 200 tests, as you would certainly need to apply a multiple testing correction for that many tests, and a moderated t statistic will have more power and fewer false discoveries than an ordinary t statistic. Cheers, Belinda -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor-bounces at r-project.org] On Behalf Of Richard Friedman Sent: Friday, 15 June 2012 2:40 AM To: Bioconductor mailing list Subject: [BioC] How many tests do you need to moderate the t-statistic in Limma Dear List, Is there a lower limit for the number of tests you need to produce a moderated t-statistic with Limma? I am now analyzing a peptide array which after filtering has about 200 present spots. Can Limma be applied to borrow power over only 200 tests? Should it be applied to this situation? Thanks and best wishes, Rich ------------------------------------------------------------ Richard A. Friedman, PhD Associate Research Scientist, Biomedical Informatics Shared Resource Herbert Irving Comprehensive Cancer Center (HICCC) Lecturer, Department of Biomedical Informatics (DBMI) Educational Coordinator, Center for Computational Biology and Bioinformatics (C2B2)/ National Center for Multiscale Analysis of Genomic Networks (MAGNet) Room 824 Irving Cancer Research Center Columbia University 1130 St. Nicholas Ave New York, NY 10032 (212)851-4765 (voice) friedman at cancercenter.columbia.edu http://cancercenter.columbia.edu/~friedman/ "School is an evil plot to suppress my individuality" Rose Friedman, age15 _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}