20
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Erratum to: ‘NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data’

      correction
      ,
      BMC Genomics
      BioMed Central

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Unfortunately, the original version of this article [1] contained an error. The authors noted an error only in the HTML version of their article. The equation (8) has a typo in it. It is shown as: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \mathrm{D}\left(\mathrm{V},\backslash,\ \mathrm{W}\ \mathrm{H}\right) $$\end{document} D V , \ , W H However it should be shown as the following: \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$ \mathrm{D}\left(\mathrm{V},\ \mathrm{W}\ \mathrm{H}\right) $$\end{document} D V , W H

          Related collections

          Most cited references1

          • Record: found
          • Abstract: found
          • Article: found
          Is Open Access

          NMFP: a non-negative matrix factorization based preselection method to increase accuracy of identifying mRNA isoforms from RNA-seq data

          Background The advent of next-generation RNA sequencing (RNA-seq) has greatly advanced transcriptomic studies, including system-wide identification and quantification of mRNA isoforms under various biological conditions. A number of computational methods have been developed to systematically identify mRNA isoforms in a high-throughput manner from RNA-seq data. However, a common drawback of these methods is that their identified mRNA isoforms contain a high percentage of false positives, especially for genes with complex splicing structures, e.g., many exons and exon junctions. Results We have developed a preselection method called “Non-negative Matrix Factorization Preselection” (NMFP) which is designed to improve the accuracy of computational methods in identifying mRNA isoforms from RNA-seq data. We demonstrated through simulation and real data studies that NMFP can effectively shrink the search space of isoform candidates and increase the accuracy of two mainstream computational methods, Cufflinks and SLIDE, in their identification of mRNA isoforms. Conclusion NMFP is a useful tool to preselect mRNA isoform candidates for downstream isoform discovery methods. It can greatly reduce the number of isoform candidates while maintaining a good coverage of unknown true isoforms. Adding NMFP as an upstream step, computational methods are expected to achieve better accuracy in identifying mRNA isoforms from RNA-seq data. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2304-8) contains supplementary material, which is available to authorized users.
            Bookmark

            Author and article information

            Contributors
            jli@stat.ucla.edu
            Journal
            BMC Genomics
            BMC Genomics
            BMC Genomics
            BioMed Central (London )
            1471-2164
            19 April 2016
            19 April 2016
            2016
            : 17
            : 296
            Affiliations
            [ ]Division of Biostatistics, University of California, Berkeley, USA
            [ ]Department of Statistics, University of California, 8125 Math Sciences Bldg, Los Angeles, USA
            [ ]Department of Human Genetics, University of California, 695 Charles E. Young Drive South, Los Angeles, USA
            Article
            2621
            10.1186/s12864-016-2621-6
            4837548
            27094977
            ac4440ca-11b1-47da-9871-b08c0159ca13
            © Ye and Li. 2016

            Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

            History
            : 15 April 2016
            : 15 April 2016
            Categories
            Erratum
            Custom metadata
            © The Author(s) 2016

            Genetics
            Genetics

            Comments

            Comment on this article