Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 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

  • #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

    Latest Articles

    Collapse

    • seqadmin
      Genetic Variation in Immunogenetics and Antibody Diversity
      by seqadmin



      The field of immunogenetics explores how genetic variations influence immune responses and susceptibility to disease. In a recent SEQanswers webinar, Oscar Rodriguez, Ph.D., Postdoctoral Researcher at the University of Louisville, and Ruben Martínez Barricarte, Ph.D., Assistant Professor of Medicine at Vanderbilt University, shared recent advancements in immunogenetics. This article discusses their research on genetic variation in antibody loci, antibody production processes,...
      Yesterday, 07:24 PM
    • seqadmin
      Choosing Between NGS and qPCR
      by seqadmin



      Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...
      10-18-2024, 07:11 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 11-01-2024, 06:09 AM
    0 responses
    24 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-30-2024, 05:31 AM
    0 responses
    21 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-24-2024, 06:58 AM
    0 responses
    25 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 10-23-2024, 08:43 AM
    0 responses
    56 views
    0 likes
    Last Post seqadmin  
    Working...
    X