Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Is it possible to do DE analysis on single tumor-normal pair with EdgeR?

    I heard that if you have multiple tumor-normal pairs, you can estimate the BCV. Then you can use this BCV to find DE genes for each individual tumor-normal pair.

    Is this true? If so, how to use BCV to find DE genes for individual tumor-normal pairs. I couldn't find that in the EdgeR manual.

    Thanks very much in advance!

  • #2
    Regardless of the software you use, a 1 vs. 1 comparison will always yield close to useless results.

    Comment


    • #3
      Thanks for your reply.

      I have another question. I currently have six pairs of lung tumor-normal pairs RNA-seq data. Suppose I later obtain another six pairs of breast tumor-control RNA-seq data. Can I mix them up for a combined analysis?

      Can you tell me why this is not ok? It seems to me even for the "same" lung tumor, there might be heterogeneity among them. Therefore it appears to me "different" cancer can be mixed. Is that correct?

      Comment


      • #4
        I suppose you could, if you're looking for commonalities between the tumors. It all depends on the biological question you want to ask.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Latest Developments in Precision Medicine
          by seqadmin



          Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

          Somatic Genomics
          “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
          05-24-2024, 01:16 PM
        • seqadmin
          Recent Advances in Sequencing Analysis Tools
          by seqadmin


          The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
          05-06-2024, 07:48 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 05-24-2024, 07:15 AM
        0 responses
        16 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 10:28 AM
        0 responses
        18 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-23-2024, 07:35 AM
        0 responses
        22 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 05-22-2024, 02:06 PM
        0 responses
        11 views
        0 likes
        Last Post seqadmin  
        Working...
        X