Can anyone here recommend any posthoc normalisation steps following deseq2 before generating Partial Least Squared Discriminant Analysis (PLSDA) and VIP (Variance of Importance Plots)?
I presume it's not appropriate to just perform this code and use it to generate a PLSDA with these counts?
Generates DeSeqDataSet Normalisedcounts and prints as CSV
dds <- estimateSizeFactors(dds) Normalisedcounts<-counts(dds, normalized=TRUE) write.csv(Normalisedcounts, file="27_Norm.csv")
Apologies if this seems like an uneducated question but I'm new to both 'big data' statistics and deseq2.