[BioC] RMA() versus expresso with RMA options

[Benjamin Milo BOLSTAD]

As of version 1.2.13 of the affy package, by default you should get the
same expression values from both rma() and expresso().

One other point I note is that you used normalize.method="qspline" in your
expresso() call. rma() does the equivalent of normalize.method="quantiles".

Thanks,

Ben


On Fri, 2 May 2003, [iso-8859-1] cmprobst wrote:

> 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
> 	[[alternate HTML version deleted]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>