[BioC] limma and normexp

[Helen Cattan]

Hi,
 
R v 2.0.1 and Limma v 1.8.15
 
Can anyone please explain to me why I get this error when trying to use
the background correct method normexp. I have no missing values and as
far as I can tell from looking at summary information this array is not
very different from all the others. Other backgroundCorrect methods work
fine.
Code with error is below.
Thanks,
 
Helen
 
library(limma)
targets=readTargets()
myfun=function(x) as.numeric(x$Flags>1) 
RG=read.maimages(targets$FileName, source="genepix", wt.fun=myfun)
RG$printer=getLayout(RG$genes)
RG$genes=readGAL("M15k4.gal")
spottypes=readSpotTypes()
RG$genes$Status=controlStatus(spottypes, RG)
RGnormexp=backgroundCorrect(RG, method="normexp", offset=50)
Corrected array 1 
Corrected array 2 
Corrected array 3 
Error in fit.normexp(foreground = RG$G[, j], background = RG$Gb[, j]) : 
        optim failure: degeneracy of the Nelder-Mead simplex
 
 
 
 

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