Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • DESeq2 Circadian Time Series without time 0

    Hello all,

    I am using DESeq2 for the following analysis:

    I have RNA-Seq data from 2 tissues and 4 time points, with 4 replicates for each condition. I have two tissues (liver and scn) and four timepoints (3,9,15,21).

    I'm trying to test for genes where time is a factor, so my full model is

    Code:
    ~ tissue + time + tissue:time
    while my reduced is simply

    Code:
    ~ tissue
    Things look good, but when the results get returned, the model has compared each timepoint to time 3:
    Code:
    > resultsNames(dds)
    [1] "Intercept"           "tissue_scn_vs_liver" "time_9_vs_3"         "time_15_vs_3"        "time_21_vs_3"       
    [6] "tissuescn.time9"     "tissuescn.time15"    "tissuescn.time21"
    Since I'm looking for evidence of circadian regulation, time 3 isn't really a baseline starting point as in the fission data from the Bioconductor rnaseqGene workflow.

    I'm thinking pairwise comparisons across time points might be better, even though the number of points is small (4).

    I'd appreciate any help in building my model better.

    Thanks!

    -John
    Last edited by jaw_bio; 09-17-2015, 06:56 AM.

  • #2
    I would suggest using an LRT with a reduced model of "~tissue+tissue:time". That would directly answer the question, "After accounting for tissue-specific differences and interactions, what genes vary with time?" It seems that that's what you're asking. This should expose the typical genes, such as core clock members used in both the SCN and liver.

    Comment


    • #3
      Originally posted by dpryan View Post
      I would suggest using an LRT with a reduced model of "~tissue+tissue:time". That would directly answer the question, "After accounting for tissue-specific differences and interactions, what genes vary with time?" It seems that that's what you're asking. This should expose the typical genes, such as core clock members used in both the SCN and liver.
      Thanks! I appreciate the response.

      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
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X