Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • analyzing RNA seq

    Hi All,

    I have RNA sequencing data (expression data) for a control sample and cases (with disease) and at multiple time points but no replicates of. any ideas on how to analyze this type of data?

    thanks

  • #2
    check out Deseq2 and Dexseq.

    Comment


    • #3
      No replicates is a bad experimental design.
      Next maSigPro: updating maSigPro Bioconductor
      package for RNA-seq time series

      and here http://www.hindawi.com/journals/bmri/2013/203681/

      Comment


      • #4
        No replicates means you have no ability to use parametric statistics to assess significance (other than using permutations or some other iterative approach to simulate=guestimate variance).

        You should have a look at some alternative analysis. Two that come to mind is a simple Rank Product analysis of fold change lists (which you can do in R or in a simple Excel spreadsheet for that matter). There is also GFOLD (http://bioinformatics.oxfordjournals...8/21/2782.long ) which uses a baseyian posterior probablity estimate of the distribution of fold changes to derive statistics and ranking. GFOLD will be helped by replicates (as they allow for a more robust estimate of the posterior probability distribution) but is valid without them (the only assumption then is that read count for any gene is poisson distributed).

        GFOLD is available in BioConductor.
        Last edited by mbblack; 07-31-2014, 06:41 AM.
        Michael Black, Ph.D.
        ScitoVation LLC. RTP, N.C.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM
        • seqadmin
          Techniques and Challenges in Conservation Genomics
          by seqadmin



          The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

          Avian Conservation
          Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
          03-08-2024, 10:41 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Yesterday, 06:37 PM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 06:07 PM
        0 responses
        10 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        51 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        68 views
        0 likes
        Last Post seqadmin  
        Working...
        X