I am going to run a differential expression analysis on raw count RNA-seq data with DESeq.
I now that with the following piece of code I can produce a normalised counts dataset,
cds <- newCountDataSet(counts, condition)
cds <- estimateSizeFactors(cds)
sizeFactors <- sizeFactors(cds)
normal_counts <- counts(cds, normalized=TRUE )
but I need to introduce a condition. So what I am wandering is: does the normalisation depend on the condition? What if I change it?
I would like to produce a normalised dataset that I can afterwards use in different analysis, analysing differential expression according to different conditions. Is it possible?
Another thing I would like to know is if I can use principal components rather than batches in my analysis, do Deseq/Deseq2 allow it?