Jenny Drnevich | 1 Nov 16:01 2005

Re: gcrma

Here is one solution to do it piece by piece, although not in expresso:

First, modify the gcrma function to just do the background correction. Type:

 > mygcrma <- edit(gcrma)

and change the last line to read:


Then call:

 >gc.affybatch <- mygcrma(raw.affybatch)

and you'll get an affybatch object with GC background corrected data.

You can then do quantile normalization on this (or any other affybatch) by 
simply calling:

 > gcnorm.affybatch <- normalize(gc.affybatch)

To just do the summarization on any affybatch, try:

gcnorm.eset <- rma(gcnorm.affybatch, background=F, normalize=F)

You can also turn off background correction and normalization in expresso, 
but the rma routine is faster. I don't think you can turn off summarization 
in expresso - see ?expresso.

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