Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • DESeq2 - paired formula design with replicates

    Hi all,

    I know that this is a frequently asked question, but I still haven't quite grasped how to build the formula design for a multifactorial paired study. My sample table is as follows:

    Has.disease PatientName Replicate Treatment Individual
    N Control 1 Ctrl 1
    N Control 1 Epi 1
    N Control 2 Ctrl 2
    N Control 2 Epi 2
    N Control 3 Ctrl 3
    N Control 3 Epi 3
    Y Patient1 1 Ctrl 1
    Y Patient1 1 Epi 1
    Y Patient1 2 Ctrl 2
    Y Patient1 2 Epi 2
    Y Patient2 1 Ctrl 1
    Y Patient2 1 Epi 1
    Y Patient2 2 Ctrl 2
    Y Patient2 2 Epi 2
    Y Patient2 3 Ctrl 3
    Y Patient2 3 Epi 3

    I'm interested in identifying those genes which have a different expression profile between disease/not-disease patients after treatment with Epi. I finally settled on a design formula of: ~Has.disease + Has.disease:Replicate + Has.disease:Treatment (per the vignette), but I really don't know 1) What exactly the formula is measuring, and 2) How I should set my corresponding contrasts.

    As an aside, I've had a very hard time understanding when I should be using the : or the * interaction term in the design formula - I've had no luck with the DESeq2 documentation or on the online forums with finding a good guideline.

  • #2
    ops.. I also want that DESeq2 treats samples as replicates but it doesnt as attached
    Attached Files

    Comment


    • #3
      This means you want to test the interaction of treatment and disease, controlling for the individuals within each disease group.

      In R formula this is:

      ~ disease + disease:replicate + treatment + disease:treatment

      Make sure that replicate is a factor, not a numeric. Make sure you set the reference level of disease and treatment using relevel() or the levels argument to factor() (see vignette).

      And you test the final term, disease:treatment. You can do this with:

      dds <- DESeq(dds, betaPrior=FALSE)
      res <- results(dds)

      The betaPrior=FALSE is recommended for designs with interaction terms. This will happen by default in the next release (Oct 2015).

      The interpretation of the interaction term is the additional effect of treatment in the disease group compared to the no disease group.

      If you are not familiar with interaction terms, and want to learn more, it's best to have a local statistician explain them (this is not specific to DESeq2 but a general concept in statistical analysis).
      Last edited by Michael Love; 07-27-2015, 09:33 AM.

      Comment


      • #4
        Thank you Michael for solving my trouble
        you are the leader

        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