Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • good "benchmark" or minimum bayes factor for differential expression?

    I'm filtering a file with genome wide analysis of bayes factors between two stages in neuron development. What's a good minimum BF for a gene to be counted as differentially expressed? In a Nature Communications paper it seems that they used BF>20, but I'm not sure if that's just for the specific study they were doing, or if that's a generally universal value.

  • #2
    In general, Bayes Factors are a bit like interpreting a p-value and the choice of cutoff for "significance" is arbitrary. The Jeffrey's scale is one widely used suggested scaling of significance where K's >10 are "strong" inidcators of significant differences, and K's > 10^2 are "decisive" indicators of significance and anything in between as "very strong" indication (that is, that gene expression levels for population M2 are greater than those for population M1, for example).

    In my experience, Bayes factors are not at all commonly used for differential gene expression, so you may need to convince an audience of the validity of the methods used to generate that file (not to mention explaining just what a Bayes factor is as most genomic biologists will have never heard of the term).
    Last edited by mbblack; 08-05-2015, 04:18 AM.
    Michael Black, Ph.D.
    ScitoVation LLC. RTP, N.C.

    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
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    9 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