Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • Sushil
    Junior Member
    • Jan 2015
    • 1
    #1

    cummeRbund MDS and PCA plot explanation

    Hello folks,

    I have limited understanding of RNA seq data analysis. I am using cufflink pipeline to analyse my RNAseq data comprising 1 treatment and 1 control. Three biological replicates in each condition. Can anybody help me whether I should trust my data based on the MDS plot? Any other suggestion to correct if there are any biases in the sample?

    Thanks
    Sushil
    Attached Files
    Tags: None
    • danwiththeplan
      Member
      • Sep 2011
      • 72
      #2
      I'm not an expert but if your replicates are closer to replicates from another condition than they are to each other, I can see a problem. Surely replicates from a single condition should cluster?

        Comment

        Previous template Next

        Latest Articles

        Collapse
        • 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
        • SEQadmin2
          New Genomics Technologies Take Aim at Long-Standing Limits
          by SEQadmin2


          Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

          We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing          ...
          09-28-2026, 10:25 AM
        View All

        ad_right_rmr

        Collapse

        News

        Collapse
        Topics Statistics Last Post
        Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
        Started by SEQadmin2, 10-22-2026, 11:13 AM
        0 responses
        23 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
        20 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-22-2026, 10:48 AM  
        Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2
        Started by SEQadmin2, 10-15-2026, 10:52 AM
        0 responses
        36 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-15-2026, 10:52 AM  
        Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2
        Started by SEQadmin2, 10-14-2026, 05:39 AM
        0 responses
        42 views
        0 reactions
        		 Last Post SEQadmin2
        by SEQadmin2
        10-14-2026, 05:39 AM  
        View All
        Working...