I found rlog transformation method in DESeq2 package was very useful for clustering RNA-seq data.
Recently, I was dealing with some time-course data, and ready to run a co-expression network analysis via a R package, which recommends a variance-stabilizing transformation. I'm wondering how to do rlog (vst) for time-course data.
For example, if I have three time-points, Day0, Day1, and Day2, shall I just take the Day0 sample as untreated sample (Day1 and Day2 sample as treated samples), then simply call the rlogTransformation function ?
Thanks so much.