MOTIVATION: With the proliferation of microarray experiments and their availability in the public domain, the use of meta-analysis methods to combine results from different studies increases. In microarray experiments, where the sample size is often limited, meta-analysis offers the possibility to considerably increase the statistical power and give more accurate results. RESULTS: A moderated effect size combination method was proposed and compared with other meta-analysis approaches. All methods were applied to real publicly available datasets on prostate cancer, and were compared in an extensive simulation study for various amounts of inter-study variability. Although the proposed moderated effect size combination improved already existing effect size approaches, the P-value combination was found to provide a better sensitivity and a better gene ranking than the other meta-analysis methods, while effect size methods were more conservative. AVAILABILITY: An R package metaMA is available on the CRAN.
MOTIVATION: With the proliferation of microarray experiments and their availability in the public domain, the use of meta-analysis methods to combine results from different studies increases. In microarray experiments, where the sample size is often limited, meta-analysis offers the possibility to considerably increase the statistical power and give more accurate results. RESULTS: A moderated effect size combination method was proposed and compared with other meta-analysis approaches. All methods were applied to real publicly available datasets on prostate cancer, and were compared in an extensive simulation study for various amounts of inter-study variability. Although the proposed moderated effect size combination improved already existing effect size approaches, the P-value combination was found to provide a better sensitivity and a better gene ranking than the other meta-analysis methods, while effect size methods were more conservative. AVAILABILITY: An R package metaMA is available on the CRAN.
Authors: Zhang Wang; Yuqiong Yang; Zhengzheng Yan; Haiyue Liu; Boxuan Chen; Zhenyu Liang; Fengyan Wang; Bruce E Miller; Ruth Tal-Singer; Xinzhu Yi; Jintian Li; Martin R Stampfli; Hongwei Zhou; Christopher E Brightling; James R Brown; Martin Wu; Rongchang Chen; Wensheng Shu Journal: ISME J Date: 2020-07-27 Impact factor: 10.302
Authors: Andrew Ratanatharathorn; Marco P Boks; Adam X Maihofer; Allison E Aiello; Ananda B Amstadter; Allison E Ashley-Koch; Dewleen G Baker; Jean C Beckham; Evelyn Bromet; Michelle Dennis; Melanie E Garrett; Elbert Geuze; Guia Guffanti; Michael A Hauser; Varun Kilaru; Nathan A Kimbrel; Karestan C Koenen; Pei-Fen Kuan; Mark W Logue; Benjamin J Luft; Mark W Miller; Colter Mitchell; Nicole R Nugent; Kerry J Ressler; Bart P F Rutten; Murray B Stein; Eric Vermetten; Christiaan H Vinkers; Nagy A Youssef; Monica Uddin; Caroline M Nievergelt; Alicia K Smith Journal: Am J Med Genet B Neuropsychiatr Genet Date: 2017-07-10 Impact factor: 3.568