Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GSEA and genes ranked by q value

    Hi guys,

    Do you know if it's correct to use GSEA preranked tool with a .rnk file composed of genes ranked by q value? (rather than fold increase, for instance). If so, are there any parameters that need to be fixed?

    Thanks a lot!

  • #2
    From GSEA manual

    "For instance, you might have used your favorite tTest-like statistic to produce a ranked ordered gene list from your dataset which you now want to test for enrichment."

    The question is, what should we include as numeric value for the second column (first corresponds to identifiers) in the .rnk file?

    Comment


    • #3
      Same question here. Do you use the q-values as the weight (class difference metric?). I use the q-value but I am not sure if I can trust the results. I will appreciate any clarification.

      Comment

      Latest Articles

      Collapse

      • seqadmin
        Recent Developments in Metagenomics
        by seqadmin





        Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...
        09-23-2024, 06:35 AM
      • seqadmin
        Understanding Genetic Influence on Infectious Disease
        by seqadmin




        During the COVID-19 pandemic, scientists observed that while some individuals experienced severe illness when infected with SARS-CoV-2, others were barely affected. These disparities left researchers and clinicians wondering what causes the wide variations in response to viral infections and what role genetics plays.

        Jean-Laurent Casanova, M.D., Ph.D., Professor at Rockefeller University, is a leading expert in this crossover between genetics and infectious...
        09-09-2024, 10:59 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 04:51 AM
      0 responses
      8 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 10-01-2024, 07:10 AM
      0 responses
      13 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-30-2024, 08:33 AM
      0 responses
      18 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 09-26-2024, 12:57 PM
      0 responses
      16 views
      0 likes
      Last Post seqadmin  
      Working...
      X