Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • GreboGuru
    Junior Member
    • Jul 2013
    • 7

    EdgeR question and looking at significant differences in fold changes.

    Hello all,
    I want to use a GLM in EdgeR on raw fragment counts generated from cuffdiff. I have 4 groups (A,B,C,D) with 4 biological replicates each. I want to determine if there is a significant difference between the fold change between A/B and the fold change C/D. So I want to look at significant differences of significant differences. I am thinking of using the following command in EdgeR:

    > my.contrast <- makeContrasts((A/B)-(C/D), levels=design)
    > lrt <- glmLRT(fit, contrast=my.contrast)

    Can anyone give me a sanity check on this?
  • dpryan
    Devon Ryan
    • Jul 2011
    • 3478

    #2
    Correct me if I'm misunderstanding, but can't this be restated as looking for interaction effects in a stereotypical 2x2 factorial design? In effect, that seems to be what you're trying to do.

    Comment

    • GreboGuru
      Junior Member
      • Jul 2013
      • 7

      #3
      Thanks for the input!
      That was also my first thought, to run a two-way ANOVA where:
      y = diet + genotype + diet*genotype
      and then any interacting effects would be cases where the diet had a significantly more pronounced effect on one genotype than the other. EdgeR should be able to handle this as well,right? There a better way to do this than an ANOVA?

      Comment

      • dpryan
        Devon Ryan
        • Jul 2011
        • 3478

        #4
        Probably a typo, but you mean "y=diet*genotype" or "y=diet+genotype+diet:genotype" (both are the same), otherwise you fit with redundant coefficients :P

        edgeR can definitely handle situations like this (as can DESeq and a few others). Have a look at the user guide for edgeR for some examples of this. I've used similar models to look at drug:genotype interactions and diet:gender interactions (mostly with DESeq, but edgeR is really similar). This is also the standard way to look for these effects, so whomever end up reviewing the paper including this data should be comfortable with this approach.

        Comment

        • GreboGuru
          Junior Member
          • Jul 2013
          • 7

          #5
          Kind of a typo - I was thinking of how it would be done in SAS. Thanks again for the tips. Alles klar!

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Pathogen Surveillance with Advanced Genomic Tools
            by seqadmin




            The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
            Yesterday, 11:48 AM
          • seqadmin
            New Genomics Tools and Methods Shared at AGBT 2025
            by seqadmin


            This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

            The Headliner
            The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
            03-03-2025, 01:39 PM
          • seqadmin
            Investigating the Gut Microbiome Through Diet and Spatial Biology
            by seqadmin




            The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...
            02-24-2025, 06:31 AM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, 03-20-2025, 05:03 AM
          0 responses
          26 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-19-2025, 07:27 AM
          0 responses
          33 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-18-2025, 12:50 PM
          0 responses
          25 views
          0 reactions
          Last Post seqadmin  
          Started by seqadmin, 03-03-2025, 01:15 PM
          0 responses
          190 views
          0 reactions
          Last Post seqadmin  
          Working...