Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • RNA-Seq: Differential expression analysis for sequence count data.

    Syndicated from PubMed RSS Feeds

    Differential expression analysis for sequence count data.

    Genome Biol. 2010 Oct 27;11(10):R106

    Authors: Anders S, Huber W

    ABSTRACT: High-throughput sequencing assays such as RNA-Seq, ChIP-Seq or barcode counting provide quantitative readouts in the form of count data. To infer diferential signal in such data correctly and with good statistical power, estimation of data variability throughout the dynamic range and a suitable error model are required. We propose a method based on the negative binomial distribution, with variance and mean linked by local regression and present an implementation, DESeq, as an R/Bioconductor package.

    PMID: 20979621 [PubMed - as supplied by publisher]



    More...

  • #2
    See this paper too:

    Differential gene and transcript expression analysis of RNA-Seq experiments with TopHat and Cufflinks.

    Trapnell et al. (2012) Nature protocols, 7:562-578

    Comment


    • #3
      Brief Bioinform. 2012 Sep 17. [Epub ahead of print]
      A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis.
      Dillies MA, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Laloë D, Le Gall C, Schaëffer B, Le Crom S, Guedj M, Jaffrézic F; on behalf of The French StatOmique Consortium.
      Abstract

      During the last 3 years, a number of approaches for the normalization of RNA sequencing data have emerged in the literature, differing both in the type of bias adjustment and in the statistical strategy adopted. However, as data continue to accumulate, there has been no clear consensus on the appropriate normalization method to be used or the impact of a chosen method on the downstream analysis. In this work, we focus on a comprehensive comparison of seven recently proposed normalization methods for the differential analysis of RNA-seq data, with an emphasis on the use of varied real and simulated datasets involving different species and experimental designs to represent data characteristics commonly observed in practice. Based on this comparison study, we propose practical recommendations on the appropriate normalization method to be used and its impact on the differential analysis of RNA-seq data.

      PMID:22988256

      Comment


      • #4
        Hi protist, wanderfull and recent work.
        It`s very interesting the SEQanswers people share good publication/papers in NGS approach.

        Thanks

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Investigating the Gut Microbiome Through Diet and Spatial Biology
          by seqadmin




          The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...
          02-24-2025, 06:31 AM
        • seqadmin
          Quality Control Essentials for Next-Generation Sequencing Workflows
          by seqadmin




          Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

          Nucleic Acid Quality Control
          Preparing for NGS starts with isolating the...
          02-10-2025, 01:58 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-03-2025, 01:15 PM
        0 responses
        46 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-28-2025, 12:58 PM
        0 responses
        167 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-24-2025, 02:48 PM
        0 responses
        525 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-21-2025, 02:46 PM
        0 responses
        256 views
        0 likes
        Last Post seqadmin  
        Working...
        X