Hi James,
Thanks for your reply. In the example you provided, the distribution is ALMOST identical, except in the region with large intensities. So I think the correct way should be that the distribution in probe set level from different arrays should be ALMOST identical, but theoretically, it could deviate from strictly identical, due to the median polish. The reason I asked this question is because I actually downloaded one dataset online which says it has been RMA normalized, but the distribution deviates from identical more than what I expect, that's why I am suspicious of the question: do different arrays have identical distribution in probe set level after RMA? 
Thanks again,
-Jim

--- On Wed, 1/20/10, James W. MacDonald <jmacdon@med.umich.edu> wrote:

From: James W. MacDonald <jmacdon@med.umich.edu>
Subject: Re: [BioC] question about RMA normalized gene expression values
To: "James Anderson" <janderson_net@yahoo.com>
Cc: bioconductor@stat.math.ethz.ch
Date: Wednesday, January 20, 2010, 1:04 PM

Hi James,

James Anderson wrote:
> Hi, 
> Do different arrays have identical distribution in probe set level after RMA normalization? Since RMA does quantile normalization in probe level, the distribution in probe level should be identical. Does the median polish summarization (which summarizes the expression value from probe level to probe set level) make the distribution different from each other? 

You can test this for yourself.

biocLite("affydata")
library(affydata)
data(Dilution)
hist(Dilution)
a <- normalize(Dilution)
hist(a)
eset <- rma(Dilution)
plotDensity(exprs(eset))

Best,

Jim


> 
> Thanks,
> 
> -James
> 
> 
> 
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-- James W. MacDonald, M.S.
Biostatistician
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University of Michigan
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