[BioC] Error with normexp in limma background correction

[Gordon K Smyth]

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