EdgeR Normalization Question

R_user

Junior Member

Join Date: Mar 2012

Posts: 1
- Share
- Tweet
#1

EdgeR Normalization Question

03-31-2012, 02:07 AM

I am looking to do TMM normalization in an experiment where you have to do pairwise comparisons between 20+ samples in replicates of three (A1, A2, A3 vs B1, B2, B3; A1, A2, A3 vs C1, C2, C3; B1, B2, B3 vs C1,C2, C3 and so on).
I was thinking that I should normalize all the samples together and then do pairwise comparisons.
I was wondering how I can get EdgeR to give me the TMM normalized values in a csv file.
Thanks!
Tags: None
Gordon Smyth

Member

Join Date: Apr 2011

Posts: 91
- Share
- Tweet
#2

05-07-2012, 10:14 PM

There's actually no such thing as TMM normalized values. Normalization in edgeR is something that affects the fitted models rather than the data values. As the edgeR User's Guide says:

"There are methods implemented in edgeR to normalize the counts for compositional bias in sequenced libraries and for differences between libraries in sequencing depth. These adjustments are offsets in the models used for testing DE and do not transform the counts in any way."
Comment

Previous template Next

Reply to Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems

by mylaser

Kheloyar – Everything You Need to Know About Kheloyaar Login and Kheoyar Id
If you are looking for an online gaming platform that offers a user-friendly experience, Kheloyar has become a name that many users search for. Whether you're interested in creating a new account, accessing your dashboard through Kheloyaar Login, or learning how to obtain a Kheoyar Id, understanding the platform's features and account process is essential.
This guide explains everything you need to know about...
- Channel: Articles
Today, 01:13 AM
Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems

by SEQadmin2

Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...
- Channel: Articles
07-09-2026, 11:10 AM
Cancer Drug Resistance: The Lingering Barrier to Rising Survival

by SEQadmin2

Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
- Channel: Articles
07-08-2026, 05:17 AM

Topics	Statistics	Last Post
New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2 Started by SEQadmin2, 07-09-2026, 10:04 AM	0 responses 16 views 0 reactions	Last Post by SEQadmin2 07-09-2026, 10:04 AM
Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2 Started by SEQadmin2, 07-08-2026, 10:08 AM	0 responses 10 views 0 reactions	Last Post by SEQadmin2 07-08-2026, 10:08 AM
Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2 Started by SEQadmin2, 07-07-2026, 11:05 AM	0 responses 22 views 0 reactions	Last Post by SEQadmin2 07-07-2026, 11:05 AM
High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2 Started by SEQadmin2, 07-02-2026, 11:08 AM	0 responses 31 views 0 reactions	Last Post by SEQadmin2 07-02-2026, 11:08 AM

Unconfigured Ad

EdgeR Normalization Question

Comment

Latest Articles

ad_right_rmr

News