Seqanswers Leaderboard Ad

Collapse
X
 
  • Filter
  • Time
  • Show
Clear All
new posts
  • dembot
    Junior Member
    • Feb 2014
    • 4

    Very basic cuffdiff normalization question

    Hi Folks --

    I'm a bit confused about the method that cuffdiff uses to normalize expression levels between the two (or more) conditions that you feed it. I generally use geometric normalization, but am unclear whether this means that normalization is dependent on the expression levels in your conditions, or whether it's tied to some independent factor that's constant regardless of what conditions you feed to cuffdiff.

    e.g. Say we have GeneX, to which we want to normalize, with FPKM in Condition 1 = 10, and FPKM in sample 2 = 20. Cuffdiff could normalize in one of two ways:

    1) Multiply all FPKM values in Condition 1 or divide all values in Condition 2 by a factor of 2, so that GeneX's FPKM is the same in both conditions.

    2) Knowing that, on average, GeneX is usually around 30, cuffdiff could multiply the FPKM's in each condition so that, again, GeneX is the same in both conditions.

    I'm curious about this because if normalization is done the first way, this means that you can only compare FPKM values between conditions that have been paired together in cuffdiff. However, if (2) is true, this means that you can compare FPKM values between conditions that were NOT directly paired in cuffdiff. Put another way, if (2) is true, this means that the FPKM value for a given gene and condition is an absolute measure of enrichment in that condition. I've noticed, generally speaking, that my FPKM value for a given gene and condition tends to be pretty stable, regardless of what other condition I pair it with in cuffdiff (e.g. GeneX from Sample 1 = 10, regardless of whether Sample 1 is paired with Sample 2 or Sample 3).

    Does this mean that, if I notice GeneY = 50 in Condition 1 (when I compare condition 1 to condition 2), but equals zero in all other conditions (e.g. condition 2 vs. 3, 4 vs. 5), that I can make any definitive statement about GeneY being higher in condition 1 than conditions 3, 4 or 5 (which I have not compared condition 1 to directly)?
    Last edited by dembot; 05-21-2014, 08:54 AM.

Latest Articles

Collapse

  • seqadmin
    Pathogen Surveillance with Advanced Genomic Tools
    by seqadmin




    The COVID-19 pandemic highlighted the need for proactive pathogen surveillance systems. As ongoing threats like avian influenza and newly emerging infections continue to pose risks, researchers are working to improve how quickly and accurately pathogens can be identified and tracked. In a recent SEQanswers webinar, two experts discussed how next-generation sequencing (NGS) and machine learning are shaping efforts to monitor viral variation and trace the origins of infectious...
    03-24-2025, 11:48 AM
  • seqadmin
    New Genomics Tools and Methods Shared at AGBT 2025
    by seqadmin


    This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.

    The Headliner
    The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...
    03-03-2025, 01:39 PM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-20-2025, 05:03 AM
0 responses
49 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-19-2025, 07:27 AM
0 responses
57 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-18-2025, 12:50 PM
0 responses
50 views
0 reactions
Last Post seqadmin  
Started by seqadmin, 03-03-2025, 01:15 PM
0 responses
201 views
0 reactions
Last Post seqadmin  
Working...