[BioC] got different gene expression data from RMA

Meiyin.Gao at unibas.ch Meiyin.Gao at unibas.ch
Wed Sep 5 15:14:13 CEST 2007


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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