Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • DESeq2DataSet Multivariate Design?

    Hello,

    I'm currently working on a project with two tumor cell lines each from a different patient, and each one of the tumor cell lines has a control and treated group. I'm trying to look at the changes in gene expression that occur in each tumor cell line between untreated and those treated with Treatment A using DESeq2, but i'm having trouble and keep getting a warning message when running the DESEq pipeline

    I'm running DESeq2 off of a Summarized Experiment:

    se <- summarizeOverlaps(features=exons, reads=list,
    mode="Union",
    singleEnd=FALSE,
    ignore.strand=FALSE,
    fragments=TRUE, BPPARAM = SerialParam())

    colData(se)=DataFrame(sample)

    For the design I used: design=~Cell + Treat + Cell:Treat

    This is the error message I get when I run the DEseq pipeline:

    >dds<-DESeq(dds)
    estimating size factors
    estimating dispersions
    gene-wise dispersion estimates
    mean-dispersion relationship
    final dispersion estimates
    fitting model and testing
    -- standard model matrices are used for factors with two levels and an interaction,
    where the main effects are for the reference level of other factors.
    see the 'Interactions' section of the vignette for more details: vignette('DESeq2')

    Is there another way to run the differential expression analysis to look at the change in expression level between the control and treated for each cell line ? I'm not sure why i keep getting this error. I've tried running DESeq2 with 1 cell line at a time (2 groups instead of 4) and I got very different results (only 5 genes instead of 81)

    Thanks!

    Lilly

  • #2
    We discourage simultaneously crossposting identical question on multiple sites.

    This duplicates the effort of the answerers (they can't see that a question was answered).

    And it also spreads out the answers, which makes it harder to other users to track the thread.

    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
    12 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