[BioC] RMA() versus expresso with RMA options

[cmprobst]

Hi, everybody,


I have analyzed a set of CEL files with rma() and with expresso(), using the following options: normalize.method=qspline, bg.method=rma, pmcorrect.method=pmonly, summary.method=medianpolish.

As probably some people are aware, the expression intensity values obtained from both methods are not identical.

What is the reason? Maybe RMA() uses rma2 as the method to correct for background values? If so, what is the difference between these two methods of background correction?

TIA

Christian
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