How to apply RLM normalization to a protein expression matrix in R?

Question

[tasjfasfankihj]

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.

Answer 1

[Mo]

I have never done this normalisation, have a look at this package, I found there is a function for RLM normalisation (page 8 here)

You can find some theory here

Here is an example of RLM in MASS package

Page 127 of this as well

Hope it helps