hi

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<-matrix(runif(nrow(dds)*ncol(dds),0.5,1.5),ncol=ncol(dds),nrow=nrow(dds),dimnames=list(1:nrow(dds),1:ncol(dds)))

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

>normalizationFactors(dds)<- normFactors

>sizeFactors(dds)<-normFactors

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

Thank you for cooperation in advance.

Parvin

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

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