[BioC] question about RMA normalized gene expression values

[James W. MacDonald]

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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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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