RMA on different disease labels

Question

[mincej20]

I'm working with HGU133Plus2 datasets, and I'm determining the best normalization procedures.

RMA seems to be the standard in literature, however some papers have been opting away from global normalization procedures:

1. https://www.nature.com/articles/s41598-020-72664-6
2. https://ieeexplore.ieee.org/document/6999142

I'm not familiar with how the statistics with RMA works. So my question is: Can I apply RMA on each disease group separately, and combine them afterwords? Or would an algorithm that accounts for disease label differences (i.e. qsmooth) be a better option?

Thanks for any help