I have a combined dataset of 123 samples and 9,482 features (expression levels of antibodies from Invitrogen's ProtoArray v5.0). Based on (http://archive.gersteinlab.org/papers/e-print/rlm/preprint.pdf), RLM normalization is the optimal method for my data. What I need help with is figuring out how to implement it in R.
PAA package says it has it, but doesn't work and the only thing I can find online about it is someone's post asking for help with no response.
Is there a way to do it with Limma's normalizebetweenarrays()?
The authors of the article I linked above apparently used the MASS package, but I haven't been able to figure out how.
Can someone please explain how to do it? Example code would be really helpful if possible.