Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • DESeq: intepreting results from interaction analysis

    Hi there,

    I am using DESeq to infer differential gene expression in a 2-factor design. Factor 1 (strain) and Factor 2 (condition) each have 4 levels; 3 bioreps each totaling to 48 samples. I am interesed in identifying an interaction effect between strain and condition, on gene expression:

    > fit1 = fitNbinomGLMs( cdsFull, count ~ strain + condition + strain : condition )
    > fit0 = fitNbinomGLMs( cdsFull, count ~ strain + condition )
    > pvalsGLM = nbinomGLMTest( fit1, fit0 )
    > padjGLM = p.adjust( pvalsGLM, method='BH' )
    > DEresults <- transform( fit1, pval=pvalsGLM, padj=padjGLM )

    Attached are results for few significant genes. I am trying to understand the fold changes and p values.
    1. How do I identify which strain and which condition have a significant interaction, ie which comparison is the padj referring to? Do I need to do pairwise comparisons of each strain against each condition?

    2. If the Intercept represents foldchange ratio of strain1 : condition1, are the other columns subtracted differences in fold change?

    I can't seem to grasp the output, any tip is greatly appreciated.

    thanks
    Attached Files

Latest Articles

Collapse

  • 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
  • seqadmin
    The Impact of AI in Genomic Medicine
    by seqadmin



    Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
    02-26-2024, 02:07 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-14-2024, 06:13 AM
0 responses
34 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-08-2024, 08:03 AM
0 responses
72 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-07-2024, 08:13 AM
0 responses
81 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-06-2024, 09:51 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X