Dear Augusto, It's fixed in Bioconductor developmental version, see https://www.stat.math.ethz.ch/pipermail/bioconductor/2008-July/023363. html Best wishes Gordon > Date: Fri, 15 Aug 2008 18:18:08 +0100 > From: Augusto Rendon <rendon at="" ebi.ac.uk=""> > Subject: [BioC] Error with normexp in limma background correction > To: bioconductor at stat.math.ethz.ch > Message-ID: <48A5BA50.1000905 at ebi.ac.uk> > Content-Type: text/plain; charset=UTF-8; format=flowed > > 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