[BioC] Adaptive background correction error

Anja Schiel a.e.schiel at lumc.nl
Mon Apr 4 12:10:48 CEST 2005

Dear all,
I tried to use the adaptive background correction for a set of 22 arrays
(2 colour). For array no 17 I get the following error

RGb<-backgroundCorrect(RG, method="normexp", offset=50)

Error in fit.normexp(foreground = RG$R[, j], background = RG$Rb[, j]) :
        optim failure: degeneracy of the Nelder-Mead simplex

There is nothing obviously wrong with that array so is it the array
that's causing the problem or something else?
And what is the Nelder-Mead simplex????

I am running R 2.0.1 + Bioconductor under Debian testing and limma

Thanks, Anja

Anja E. Schiel, Ph.D.
Departments of General Internal Medicine and Human Genetics
Leiden University Medical Center
PO Box 9503
2300 RA Leiden
The Netherlands 
tel: -31-(0)71-5276067
fax: -31-(0)71-5276075

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