Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • clinical RNA-Seq: batch effect

    Hi all,
    I have RNA-Seq data set coming from a clinical trial. The samples were extracted and sequenced at different days. That is, each individual sample could be processed separately. When a sample is available, it could be put together with other samples in other projects and run on the sequencer.

    Do you have an idea how to effectively remove the batch effect?
    Any advice will be appreciated.

  • #2
    There are packages designed for this, e.g. SVA.
    I will include batch as a covariate in the statistical model.
    Take a look at this thread: http://seqanswers.com/forums/showthread.php?t=44083

    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,”...
      Today, 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, Today, 07:15 AM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 10:28 AM
    0 responses
    15 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 07:35 AM
    0 responses
    16 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 05-22-2024, 02:06 PM
    0 responses
    8 views
    0 likes
    Last Post seqadmin  
    Working...
    X