Seqanswers Leaderboard Ad



No announcement yet.
  • 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


    • #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.


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


        Latest Articles


        • seqadmin
          Exploring the Dynamics of the Tumor Microenvironment
          by seqadmin

          The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
          07-08-2024, 03:19 PM
        • seqadmin
          Exploring Human Diversity Through Large-Scale Omics
          by seqadmin

          In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
          06-25-2024, 06:43 AM





        Topics Statistics Last Post
        Started by seqadmin, 07-10-2024, 07:30 AM
        0 responses
        Last Post seqadmin  
        Started by seqadmin, 07-03-2024, 09:45 AM
        0 responses
        Last Post seqadmin  
        Started by seqadmin, 07-03-2024, 08:54 AM
        0 responses
        Last Post seqadmin  
        Started by seqadmin, 07-02-2024, 03:00 PM
        0 responses
        Last Post seqadmin