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. Best regards Parvin