Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • edgeR multiple testing

    Hi everybody,

    I've searched a lot but have not found a definitive discussion on this yet.

    I'm using edgeR on a human dataset with 3-4 replicates per group.

    When I follow the edgeR tutorial and export (see code below) I get this:

    Code:
    dispersion = estimateCommonDisp(DGE_timepoints)
    de.com <- exactTest(dispersion, c("healthy-control","disease"))
    out_tags1 = topTags(de.com, n=length(de.com))
    write.table(out_tags1, "out_unadjusted_pvalue.csv", sep="\t")

    gene table.logConc table.logFC table.PValue table.FDR adjust.method
    ENSG00000250644 -20.0951079864 -11.2384935084 1.19615633839674e-08 0.0002112173 BH
    ENSG00000176994 -33.1995219248 -33.633064638 1.27917856074067e-07 0.0009680458 BH

    Note that adjust method is BH, but I am not sure if Pvalue adjustment was carried out by default. In the manual it seems to suggest a further Pvalue adjustment is needed:

    Code:
    # P values adjusted by Benjani-Hochberg method, single column
    out_tags_adjusted = p.adjust(de.com$table$p.value, method="BH")
    
    write.table(out_tags_adjusted, "out_adjusted_pvalue.csv", sep="\t")
    However, the two top results above then get an "adjusted" Pvalue of 1 and 0.3 respectively, and virtually no hits are significantly differently regulated.

    I guess that the initial step is sufficient to implement multiple testing.
    Comments?

  • #2
    You don't need to do any more adjustment. The adjusted values are in the column which is called 'table.FDR'.

    Comment


    • #3
      Ah I see. Thanks for the help!

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Exploring the Dynamics of the Tumor Microenvironment
        by seqadmin




        The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
        07-08-2024, 03:19 PM
      • seqadmin
        Exploring Human Diversity Through Large-Scale Omics
        by seqadmin


        In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
        06-25-2024, 06:43 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Today, 07:20 AM
      0 responses
      14 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-16-2024, 05:49 AM
      0 responses
      34 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-15-2024, 06:53 AM
      0 responses
      38 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 07-10-2024, 07:30 AM
      0 responses
      41 views
      0 likes
      Last Post seqadmin  
      Working...
      X