Question: What Are The Best Normalization Methods For Ngs Data
2
gravatar for jack
5.5 years ago by
jack420
jack420 wrote:

Hi all,

I have raw count RNA seq NGS data, I want normalize it and apply machine learning and data mining algorithms on it. I want to know that, what are the bests or suitable normalization methods are specific for this kind of data?

ADD COMMENTlink modified 11 months ago by 15617759110 • written 5.5 years ago by jack420
1

Check Optimal Scaling of Digital Transcriptomes

ADD REPLYlink written 5.5 years ago by JC7.8k

Hi jack, I am doing similar works as you do before,and I also meet the problem of which methods to adopt for normalization of different kinds of RNA-seq count for a subsequent machine learning .And have you get the solution?Could you give me some advices?

ADD REPLYlink written 11 months ago by 15617759110
2
gravatar for Ashutosh Pandey
5.5 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

A recent paper has evaluated different normalization methods. A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis http://bib.oxfordjournals.org/content/14/6/671.full.html?etoc

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Ashutosh Pandey11k
1

The conclusion of this paper is basically DESeq or EdgeR methods (TMM) were the best, and fairly similar.

Recently we had some data that was normalized much better with TMM/EdgeR than DESeq, so you may want to try both.

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Madelaine Gogol5.1k
1

imho, they are both quite similar since both of them use negative binomial distrib. for modelling. If you are not satisfied you can also check out DEGSeq. It uses poisson, we used it for first analysis and found that it is kind of more conservative. Switched to DESeq, though.

ADD REPLYlink written 5.5 years ago by Phil S.660
1
gravatar for Ying W
5.5 years ago by
Ying W3.9k
South San Francisco, CA
Ying W3.9k wrote:

This recent comparison of methods paper for RNA-seq also covers normalization: http://www.ncbi.nlm.nih.gov/pubmed/23497356

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Ying W3.9k
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