[BioC] got different gene expression data from RMA
bcarvalh at jhsph.edu
Wed Sep 5 15:29:41 CEST 2007
normalization comes before summarization (median polish).
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",
> 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
> 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!
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