Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Common Dispersion in EdgeR

    Hi all,

    I had a question about the common dispersion in EdgeR. In the manual it gives the following..

    > sqrt(d$common.disp)
    [1] 0.416

    The square root of the common dispersion gives the coefficient of variation of biological variation (BCV). Here the BCV is 41%

    However in my own dataset...
    > sqrt(y$common.disp)
    [1] 2.096939


    So is the BCV for my dataset 200%? Is this even possible?

    Edit: Am I correct in saying that this would mean the true abundance for each gene can vary by up to 200% between samples?

    I want to be able to use this for the RNASeqPower bioconductor package. Now the version of EdgeR I'm using is 3.8.2 and the manual is for 3.7.17 on the bioconductor site, maybe there is a difference between versions.. but this is the manual that the package calls.

    Thanks.
    Last edited by bob-loblaw; 10-21-2014, 06:01 AM.

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
51 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