Unconfigured Ad

Collapse
X
 
  • Time
  • Show
Clear All
new posts
  • vsmuir
    Junior Member
    • Oct 2016
    • 3

    #1

    Limma selectModel output

    I've been given a large RNAseq dataset on a biological process which I know little about. There is a ton of associated sample data, and I've built a ton of different linear models that include variables that correlate with my process of interest in either the literature or some basic, exploratory analyses.

    I'd like to figure out which of these models is worth playing around with while I learn more about the new field. My prior RNAseq analysis experience was all in really simplistic experimental systems, so I'm wondering how to appropriately apply tools like Limma's selectModel AIC/BIC criteria.

    Specifically, what is pref? How's it calculated? How should I interpret it?
    The two folks that I've spoken to have opposing opinions: One thinks that pref is a broad information criterion score and that I should pick whatever model has the lowest value in this table. The other has told me that the values indicate the number of genes fit well by each model and that I should select the model with the highest value in this table.

    As per the manual:
    IC
    matrix of information criterion scores, rows for probes and columns for models
    pref
    factor indicating the model with best (lowest) information criterion score
  • Dario1984
    Senior Member
    • Jun 2011
    • 166

    #2
    The other has told me that the values indicate the number of genes fit well by each model and that I should select the model with the highest value in this table.
    That is the correct explanation.

    Comment

    Latest Articles

    Collapse

    • SEQadmin2
      Beyond CRISPR/Cas9: Understand, Choose, and Use the Right Genome Editing Tool
      by SEQadmin2



      CRISPR/Cas9 sparked the gene editing revolution for both research and therapeutics.1 But this system still showed severe issues that limited its applications. The most prominent were the heavy reliance on PAM sequences, delivery limitations, double-stranded breaks that prompt unintended edits and cell death, and editing inefficiency (both in targeting and in knock-in reliability).

      Despite this, “CRISPR helped turn genome editing from a specialized technique into
      ...
      07-31-2026, 11:01 AM
    • SEQadmin2
      Proteomic Platforms: How to Choose the Right Analytical Strategy to Improve Detection and Clinical Applications
      by SEQadmin2


      Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.

      The systematic characterization of the human proteome has
      ...
      07-20-2026, 11:48 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by SEQadmin2, 08-13-2026, 12:22 PM
    0 responses
    20 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 08-11-2026, 10:35 AM
    0 responses
    16 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 08-06-2026, 07:41 AM
    0 responses
    32 views
    0 reactions
    Last Post SEQadmin2  
    Started by SEQadmin2, 08-03-2026, 10:13 AM
    0 responses
    50 views
    0 reactions
    Last Post SEQadmin2  
    Working...