Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • edgeR calculate CPM instead of lof2FC

    Dear, SEQanswer community,

    I want to detect differentially expressed genes between tumor and normal
    tissue, adjusting for any differences between the patients.
    I have 8 leukemia patients and 8 healthy donors.
    I follow the edgeR manual, particularly case study at chapter 4.1.

    I use the following commands:
    Code:
    > fit <- glmFit(counts, design)
    > lrt <- glmLRT(fit)
    > topTags(lrt)
    > colnames(design)
    > o <- order(lrt$table$PValue)
    > cpm(counts)[o[1:10],]
    This provides me top 10 CPM values for each of my sample. However, my goal is to get the log2FC for each sample.

    In what way I can calculate log2FC for each sample instead of CPM values in edgeR?

    Thank You very much for help!

    Olha
    Last edited by Olha; 02-10-2016, 03:10 PM. Reason: incorrect title

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
11 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
67 views
0 likes
Last Post seqadmin  
Working...
X