Question: GC content and length bias in RNA-seq data
gravatar for parvin.shariaty
26 days ago by
parvin.shariaty0 wrote:


I have seven RNA-seq data in two groups( control,treat) that produced from two companies (controls=BGI,treats=novogen). I used NOISeq to quality control of count data, and the results recommended normalization for GC content and length. But I have studied some papers and have founded that GC content and length normalization in gene expression comparison between two groups introduced bias. So I would like to use normalization factors instead of size factors in DESeq2(as described in differential analysis of count data - the DESeq2 package).


>normFactors<- normFactors / exp(rowMeans(log(normFactors)))

>normalizationFactors(dds)<- normFactors


Is it a correct manner to normalization and introduce the normalization factors in DESeq2? 

Thank you for cooperation in advance.



ADD COMMENTlink modified 24 days ago by Michael Love16k • written 26 days ago by parvin.shariaty0
gravatar for Michael Love
24 days ago by
Michael Love16k
United States
Michael Love16k wrote:

The last line does nothing, and can be skipped. The rest is correct. (Except the runif(), presumably there just for demonstration.)

BTW, to notify the developers of a post here, you can add the package name as a tag. This will trigger an email to the maintainer.

ADD COMMENTlink modified 24 days ago • written 24 days ago by Michael Love16k
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