Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • [DESeq] baseMean

    I would like to ask how exacly baseMean is calculated in DESeq.

    According to the manual from 2012-07-24 (http://tinyurl.com/8krvbny) the meaning of the three baseMean columns is:

    baseMean mean normalised counts, averaged over all samples from both conditions
    baseMeanA mean normalised counts from condition A
    baseMeanB mean normalised counts from condition B
    I interpret this as:
    Code:
    baseMean = (baseMeanA + baseMeanB) / 2
    However I have this result from a DE test which I did with DESeq (only first entry shown):
    Code:
    id	baseMean	baseMeanA	baseMeanB	foldChange	log2FoldChange	pval	padj
    geneA	4.6870306180134	3.72258134619134	6.1337045257465	1.64770194532405	0.720455295377725	0.137300747770432	0.461541670327437
    Code:
    (3.72258134619134+6.1337045257465)/2 == 4.928143
    4.928143 != 4.6870306180134
    There is obviously a discrepancy. Maybe I am interpreting it wrong.

    I'd be thankful if someone could explain how I can replicate the calculation of baseMean.

    P.S.: I asked a similar question in May this year. Simon nicely answered me that:
    Yes, it is the normalized count, i.e., simply the number of reads divided by the size factor (normalization constant) of the sample
    However, I do not know how I can get the "size factor" from the results table. If at all possible, I want to recompute baseMean given only baseMeanA and baseMeanB (is this even possible?). Because this way I wouldn't need to determine the sizeFactor.
    Last edited by Azazel; 09-09-2012, 04:45 PM. Reason: Added a PS for clarification.

  • #2
    1. Maybe you have different numbers of samples in your two conditions. Then, the base mean will not be the average of the two per-condition means.

    2. You real problem seems to be that you do not know how to get the size factors. If so, why do you not ask about this? Simply use the accessor function 'sizeFactors' on your CountDataSet to get a vector of size factors.

    Comment

    Latest Articles

    Collapse

    • 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
    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM

    ad_right_rmr

    Collapse

    News

    Collapse

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