Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Pre-process. data reduction : statistical refinement with glm

    Dear community,

    My question is about statistics.

    I have a complex experimental dataset (hundreds of samples) in which I want to test several factors and crossed factors. I know that before running any statistical test, it is very common to reduce the library sizes (which are about 2500 transcripts per sample) by applying a filtering step on the fold-change. However, fold-change is tricky in my context since it should be done between two conditions of a factor, but I want to test for multiple factors and their interaction (eg: y ~ factorA + factorB + factorA:factorB + factorC).

    So, to cope with this, I was considering to filter the library sizes by performing what I call a "statistical refinement", i.e., performing a first statistical test with the complete GLM model and from this I would subset all transcripts having p<0.05 for at least one of the factors (not padj).

    It has the effect of reducing my library size to approximately 800 transcripts, which is, I think reasonable to perform my second statistical trial. From this second statistical trial, I will then consider deferentially expressed genes to be statistically significant when padj<0.05 for the corresponding factors.

    I have not found studies having processed the data in a similar manner so I would like to know what is your opinion about such method. In my opinion, filtering steps are essential but (i) fold-changes filters are not always relevant (a small fold change of a transcript with very small variability across conditions could have dramatic biological effects and so should not be disregarded), (ii) fold change filters are appropriate only within a simple design (ie, 1 factor with 2 levels, eg: exposed vs non exposed), (iii) otherwise statistical refinement may be a good option to consider.

    Many thanks in advance for your constructive arguments and if you have the references of studies showing similar methods (I have not found yet).

    Kind regards

Latest Articles

Collapse

  • 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
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, Yesterday, 06:37 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, Yesterday, 06:07 PM
0 responses
10 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
51 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
68 views
0 likes
Last Post seqadmin  
Working...
X