edgeR normalization via TMM method

Dear all,

Could you please clear me how edgeR solve the compositional bias within an RNA-seq library via TMM method? if it removes the highly expressed genes or if it allocates lower weight (via the normalization factor of less than 1) to them?

Thanks

rna-seq edger normalization tmm

• 1,872 views • link

updated 5.9 years ago by ATpoint

• written 5.9 years ago by seta

1 answer

StatQuest is the answer:

• 0 views • link

written 5.9 years ago by ATpoint

Thank you for the great video. However, I have some questions, hope to find the answer.

In the video, he says “edgeR filters out the biased genes based on their log differences”, then he calculates the log2 (reference, gene 1/ sample 2, gene1). Here, I got confused about 1) why the ratio calculated relative to sample 2, not the reference sample?

2) Also, could you please tell me how “the weighted average of the log2 ratio” (step 4) was calculated?

3) Sorry, at Step 5, is the weighted average of log2 value multiplied by 2 to convert the value to normal value? What does mean “normal numbers”, here?

Thank you in advance

• 0 views • link

written 5.8 years ago by seta

More posts like this

Gene transcription determination with RNA-seq data
written 4.5 years ago by chansik •

I'm analyzing RNA-seq data with TMM normalization (EdgeR). The normalized TMM values of genes vary from -5.38 to 13.0, as TMM is a log scale, …
Between sample normalization using TMM approach in edgeR
written 4.6 years ago by OdongoR89 •

While performing between sample normalization using the TMM approach in edgeR (since TMM approach relies on log2FC between groups defined in the experimental design matrix) …
TMM followed by inverse normal transform
written 4.9 years ago by joseph.a.decorte •

Hey all, I am following a protocol from a paper that uses the following pre-processing procedure: > a. Read counts were normalized between samples using …
Makes sense to conduct SALMON mapping followed by NOIseq for differential expression analysis?
written 5.8 years ago by YEODYNASTY •

Dear all, For my RNA-seq project, I'll like to use SALMON to obtain GC bias-corrected count table from my fastq files. Since SALMON does not …
RNA seq data analysis and building co expression network
written 6.2 years ago by siu

Hi all, I have some questions regarding RNA seq analysis if you can suggest anything it will help me a lot. 1. I am currently …
lncRNA differential expression analysis
written 6.3 years ago by seta

Dear all, I'm busy with an RNA-seq analysis of case and control samples and got some differentially expressed coding genes and long non-coding RNA (lncRNA) …
RNA-Seq variant calling dependent on expression?
written 10.2 years ago by Dave Tang

If a deleterious variant, such as a stop gain, leads to the degradation of the mRNA via nonsense-mediated decay, it would be impossible to call …
TMM normalisation on a subtset of the data
written 10.6 years ago by tomasscheitel •

Hi, I'm working on a RNA-Seq dataset and would like to use the TMM normalization from the edgeR package to normalize the data. I have …
Within-sample comparison of TMM normalized values?
written 11.7 years ago by Ekarl2

I have the following RNA-seq set-up: - 5 samples for comparison - matrix with TMM-normalized FPKM values Now, TMM-normalization allows comparison across samples, so I …
Rna Composition Bias In Rna-Seq Analysis
written 12.8 years ago by narges •

<p>Hi,</p> <p>Normalization is one of the most important primary steps before running RNA-seq analysis. One of the biases which normalization methods try to solve is …