I am working on a survival analysis using the RMA normalized/transformed data of some cancer patients.
Here is a quick overview on RMA: http://www.molmine.com/magma/loading/rma.htm
As mentioned in the link above, RMA is already log-2 transformed and quantile normalized(skewed), so when I tried to calculate z-scores using these RMA values, it was not working (I am not getting a mean of zero when I check the summary of the global z-scores, although I have re-calculated them multiple times). Hence, I did my survival analysis (Cox regression) with the RMA values itself.
But the problem I am now running into is that without calculating z-scores, I am not sure how to establish what constitutes of high/low expression using just the RMA data, which I need to do in order to create Kaplan-Meier curves and do further analysis. Do I establish this cutoff/range using the mean/median along with the hazard ratio, or is there some other more statistically accurate way?
Any help would be greatly appreciated, thank you!