Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • DESeq2 multi-factor designs

    I am getting started with DESeq2. I am trying to understand how multi-factor design works. This is fairly basic question, but I can't find the proper answer.

    From the vignette:
    Code:
    We can account for the different types of sequencing, and get a clearer 
    picture of the differences attributable to the treatment. As condition is the 
    variable of interest, we put it at the end of the formula. Here we
    
    design(dds) <- formula(~ type + condition)
    dds <- DESeq(dds)
    So how exactly are the two parameters treated? What do the significant genes in the results mean? Are they the ones that are changing in condition regardless of type, or the ones that are changing in both type and condition? What happens when you have three or more parameters?

    Additionally, although results for condition are output by default, results for type can be retrieved as well. Does the order or parameters only matter for the output or is the test performed differently?

  • #2
    The normal phrasing for that would be "differences due to type when controlling for condition" for the "type" results and "differences due to condition when controlling for type" for the "condition" results. The syntax is the same as is used for other linear and generalized linear models in R, so that's why it's not described in depth. If "condition" has levels "A", "B", and "C", then (generally) "A" will be treated as the baseline level and you get statistics for the "BvsA" and "CvsA" comparisons (I think the most recent version of DESeq2 implements contrasts, so you can then test whatever you really want).

    Comment


    • #3
      Originally posted by dpryan View Post
      The normal phrasing for that would be "differences due to type when controlling for condition" for the "type" results and "differences due to condition when controlling for type" for the "condition" results. The syntax is the same as is used for other linear and generalized linear models in R, so that's why it's not described in depth. If "condition" has levels "A", "B", and "C", then (generally) "A" will be treated as the baseline level and you get statistics for the "BvsA" and "CvsA" comparisons (I think the most recent version of DESeq2 implements contrasts, so you can then test whatever you really want).
      That was very helpful.

      I think you misunderstood the part of my question regarding multiple parameters, though. What happens when the design goes from formula(~ x + y) to formula(~ x + y + z)?

      Comment


      • #4
        Ah, with more parameters things are the same. You're always testing one thing while accounting for the others.

        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, 03-27-2024, 06:37 PM
        0 responses
        12 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-27-2024, 06:07 PM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-22-2024, 10:03 AM
        0 responses
        53 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 03-21-2024, 07:32 AM
        0 responses
        69 views
        0 likes
        Last Post seqadmin  
        Working...
        X