Hello,
I just started analysis of RNA Seq Data (bulk - whole genome). I was trying to normalize data using limma package (voom). Is it correct to create a DGE list, then use calcNormFactors (method TMM) and then voom (normalize = none)? I've went through different papers, but I'm not really sure which is better to use. After doing some plots on normalized data, I would say, this one looks the best. However I still have problems with making a heatmap for downgenes (it was only working for upgenes). I was also working on DESeq2, and then using vst function on dds object. Is it okay if I use varianceStabilizingTransformation on a dds object to do heatmaps for upregulated genes and gene set enrichment, but I would use getVarianceStabilizedData to do WGCNA analysis? What is the difference between them? Which one should I decide on? Thank you for your help
