
I am now trying to get the probe level values from RMA, since I want to adjust 
the batch effect in probe level instead of probe set level. However, 
justRMA seems to do everything until the probe set level. What I want to do 
is to use RMA to obtain probe level expression matrix, then adjust the batch 
effect, then using median polish to get probe set level. 
Does anybody know how to circumvent the memory problem if 
I only want to get the probe level matrix? 

Many thanks,

James

       
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