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)))
Is it a correct manner to normalization and introduce the normalization factors in DESeq2?
Thank you for cooperation in advance.