[BioC] got different gene expression data from RMA

[Benilton Carvalho]

normalization comes before summarization (median polish).
b

On Sep 5, 2007, at 10:14 AM, 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.
>
> 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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