I am a beginner in R. I am currently working on gene expression data (Nanostring). The data is normalized, house-keeping genes and low abundance have been removed and the data have been log2 transformed.
I have done DE analysis with limma.
Question: do I need to use scale(data) before running the analysis? I tried both scaling and without and the result are pretty similair but there are some differences. Same goes when I did PCA, the results rate almost same but not quite.
Main question: does one always have to use scale() on the data (even normalized, log2 transformed)? Can scale() ever ”damage” the results/data?