[BioC] got different gene expression data from RMA

[James W. MacDonald]

Meiyin.Gao at unibas.ch wrote:
> I have one problem for the RMA!
> 
> I got three datasets using different RMA way in R:
> 
> from the .CEL files,
> 
> 1, justRMA()
> 
>    d <- ReadAffy()
> 2, expresso(d, bgcorrect.method="rma", normalize.method="quantiles",
>               pmcorrect.method="pmonly", summary.method="medianpolish")
> 3,
> 
>  bgd <- bg.correct(d,method="rma")
>  probes <- pm(bgd)
>  expression <- generateExprVal.method.medianpolish(probes)$exprs
>  data <- normalize.quantiles(expression)
> 
> As the results, I got three datasets. I was thinking that these three datasets
> should be identical because they were obtained from the same procedures!
> 
> But, the first and second gene expression data are identical,  the third gene
> expression data are different with the other two.

In the first two cases you are doing a quantile normalization first 
(using the PM data). In the third case you are normalizing after the 
median polish step.

Best,

Jim


> 
> Why the third data expression is different? How I can progress and get the data
> the same as the first two datasets!
> 
> Thanks a lot, and I am looking forward to hearing the solution soon!
> regards,
> meiyin
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623