[BioC] Error with normexp in limma background correction
Augusto Rendon
rendon at ebi.ac.uk
Fri Aug 15 19:18:08 CEST 2008
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
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