[BioC] Error with normexp in limma background correction

[Augusto Rendon]

Hello,

I am having a strange error message when calling backgroundCorrect with 
normexp in limma:

Error in if (all(abs(delta) < 0.0000000001)) break :
missing value where TRUE/FALSE needed

I was able to track the error to the call to optim within normexp.fit 
but that is as far as I got. Unfortunately, it is particular to this 
array, as for other datasets on the same platform it works fine. Not 
sure how to attach a 200mb file to this post.

I am working with an agilent 2 color array for chip-on-chip. The 
features were extracted with agilent's feature extraction software. 
Other background correction options work fine, including rma.

The code:

array <- read.maimages(files=file, source="agilent",columns= list( R = 
"gMeanSignal", G ="rMeanSignal", Rb ="gBGMedianSignal", Gb = 
"rBGMedianSignal"),other.columns=c("PositionX","PositionY"))

array.norm <- backgroundCorrect(array,method="normexp")

the output:
Green channel
Error in if (all(abs(delta) < 0.0000000001)) break :
missing value where TRUE/FALSE needed

Any idea?

Many thanks,

augusto

-- 
Augusto Rendon PhD
Research Associate
Department of Haematology, University of Cambridge
& National Health Services Blood and Transplant Cambridge
Long Road
Cambridge
CB2 2PT
Phone at EBI: +44 (0) 1223 49 4690
Phone at BSU: +44 (0) 1223 330 372