I have been using Deseq2 to analyze a dataset I have and ran into a problem I am not sure how to solve.
I have been using the following code to run deseq2 on my dataset:
dds <-DESeqDataSetFromMatrix(countData = ep,colData = cp,design = ~Risk)
dds <- estimateSizeFactors(dds)
rld <- rlog(dds)
vsd <- varianceStabilizingTransformation(dds)
The two PCA plots I got look completely different, so I am not sure which transformation I should rely on for further analysis.