Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • 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

  • #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

    • seqadmin
      Essential Discoveries and Tools in Epitranscriptomics
      by seqadmin




      The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
      Yesterday, 07:01 AM
    • seqadmin
      Current Approaches to Protein Sequencing
      by seqadmin


      Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
      04-04-2024, 04:25 PM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 04-11-2024, 12:08 PM
    0 responses
    58 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 10:19 PM
    0 responses
    53 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-10-2024, 09:21 AM
    0 responses
    45 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 04-04-2024, 09:00 AM
    0 responses
    55 views
    0 likes
    Last Post seqadmin  
    Working...
    X