Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • bob-loblaw
    Member
    • Jun 2012
    • 59
    #1

    DESeq2 ntop set to 500?

    Hi all,

    I was just making some PCAs and I noticed that the plotPCA function within DESeq2 only takes the 500 genes with the highest variance. I was wondering if anyone knows what is the justification for this? vs taking the whole dataset? Is it just an attempt to filter out noise?

    I'm working on a mouse RNA-Seq dataset at the moment and the plots look quite different if I take 500 genes vs taking 1000 genes
    Tags: deseq2, pca plot
    Previous template Next

    Latest Articles

    Collapse
    • SEQadmin2
      16S/ITS Profiling vs. Shotgun Metagenomics: What Changes in Your Workflow?
      by SEQadmin2




      NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification, detection...
      Today, 06:46 AM
    • SEQadmin2
      Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
      by SEQadmin2



      Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

      Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating      ...
      10-14-2026, 09:55 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    Genome Sequencing Reveals Large, Repeat-Rich DNA in Trapdoor Spider Named for Stephen Colbert by SEQadmin2
    Started by SEQadmin2, 10-28-2026, 09:57 AM
    0 responses
    22 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    10-28-2026, 09:57 AM  
    Single-Cell Sequencing of 5 Million Immune Cells Links Genetic Variants to Disease by SEQadmin2
    Started by SEQadmin2, 10-28-2026, 09:51 AM
    0 responses
    15 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    10-28-2026, 09:51 AM  
    Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
    Started by SEQadmin2, 10-22-2026, 11:13 AM
    0 responses
    68 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    10-22-2026, 11:13 AM  
    Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
    Started by SEQadmin2, 10-22-2026, 10:48 AM
    0 responses
    48 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    10-22-2026, 10:48 AM  
    View All
    Working...