[BioC] Question about R and expresso()

[Rafael A. Irizarry]

i dont fully understand your email, but im guessing the function 

mas5 

may be what you are looking for. mas5 basically does
 
expresso(data,bgcorrect.method="mas",pmcorrect.method="mas",
	 normalize=FALSE,summary.method="mas",...) 

but it also normalizes using the function: affy.scalevalue.exprSet

rafael
ps - data is a function in R's base package. i prefer using  Data or 
mydata.


On Mon, 16 Jun 2003, Daniel ~ wrote:

> 
> Hi,
> 
> We tried expresso() in R, but with bad luck.
> 
> >eset <- expresso(data, bgcorrect.method="mas", normalize.method="qspline", 
> >pmcorrect.method="subtractmm", summary.method="playerout")
> background correction: mas
> normalization: qspline
> PM/MM correction : subtractmm
> expression values: playerout
> background correcting...done.
> normalizing...[1] "samples= 100 k= 5 first= 0"
> Error in rep(data, t1) : invalid number of copies in "rep"
> In addition: Warning message:
> 'k' found is non-sense. using default in: 
> normalize.qspline(t(intensity(abatch)), ...)
> >
> 
> 
> In R we want to imitate the .CHP file we get from an .CEL file in
> Affymetrix Microarray Suite. Is there anyone that know how to tweek
> the parameters in expresso() to reach that result?
> 
> Best regards
> Daniel Marcus
> 
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