Hi,

I am attempting to preprocess 2000 samples on the HGU133 Plus 2 array. I
have 16 batches of data, ranging in size between 50 to 200 samples.

I was under the impression that using fRMA with the random effects model
would be best (over median polishing or others) because it would help
compensate for batch effects at the same time. However, I am limited in
that I cannot read 200 CEL files into memory to do the processing. I was
wondering:

a) if there was a function or method similar to that of justRMA() for fRMA.
I have read through all fRMA documentation and not found anything.

b) what my best alternative would be. Right now I was thinking that I could
run fRMA (median polishing) or SCAN.UPC (which one would be better?) on the
samples individually and then use COMBAT to counter any batch effects.
Please let me know if this would be an appropriate course of action.

Thanks for your help!

Sam

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