[BioC] Question about R and expresso()

Daniel ~ demarcus at hotmail.com
Mon Jun 16 16:50:59 MEST 2003


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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