[BioC] Adaptive background correction error

[Gordon Smyth]

>Date: Mon, 04 Apr 2005 12:10:48 +0200
>From: Anja Schiel <a.e.schiel at lumc.nl>
>Subject: [BioC] Adaptive background correction error
>To: bioconductor at stat.math.ethz.ch
>
>Dear all,
>I tried to use the adaptive background correction for a set of 22 arrays
>(2 colour). For array no 17 I get the following error
>
>RGb<-backgroundCorrect(RG, method="normexp", offset=50)
>
>Error in fit.normexp(foreground = RG$R[, j], background = RG$Rb[, j]) :
>         optim failure: degeneracy of the Nelder-Mead simplex
>
>There is nothing obviously wrong with that array so is it the array
>that's causing the problem or something else?

Adaptive background correction requires an iterative algorithm to estimate 
the background, and this algorithm sometimes fails. It is unlikely to be a 
problem with your data. This problem has been discussed before on this 
mailing list -- search the archives for "normexp".

Newer versions of limma use a different iterative algorithm to estimate the 
"normexp" background. Try upgrading and see if the new version works for you:

    install.packages("limma")

>And what is the Nelder-Mead simplex????

The online help tells you that the Nelder-Mead simplex algorithm is being 
used for the optimization -- follow the link which says "for more details 
see fit.normexp". You do not need to know the details of the algorithm.

Gordon

>I am running R 2.0.1 + Bioconductor under Debian testing and limma
>1.8.16
>
>Thanks, Anja
>
>
>--
>Anja E. Schiel, Ph.D.
>Departments of General Internal Medicine and Human Genetics
>Leiden University Medical Center
>PO Box 9503
>2300 RA Leiden
>The Netherlands
>tel: -31-(0)71-5276067
>fax: -31-(0)71-5276075