Hi,
R v 2.0.1 and Limma v 1.8.15
Can anyone please explain to me why I get this error when trying to
use
the background correct method normexp. I have no missing values and as
far as I can tell from looking at summary information this array is
not
very different from all the others. Other backgroundCorrect methods
work
fine.
Code with error is below.
Thanks,
Helen
library(limma)
targets=readTargets()
myfun=function(x) as.numeric(x$Flags>1)
RG=read.maimages(targets$FileName, source="genepix", wt.fun=myfun)
RG$printer=getLayout(RG$genes)
RG$genes=readGAL("M15k4.gal")
spottypes=readSpotTypes()
RG$genes$Status=controlStatus(spottypes, RG)
RGnormexp=backgroundCorrect(RG, method="normexp", offset=50)
Corrected array 1
Corrected array 2
Corrected array 3
Error in fit.normexp(foreground = RG$G[, j], background = RG$Gb[, j])
:
optim failure: degeneracy of the Nelder-Mead simplex
[[alternative HTML version deleted]]
> Date: Tue, 11 Jan 2005 12:52:15 -0000
> From: "Helen Cattan" <helen.cattan@jenner.ac.uk>
> Subject: [BioC] limma and normexp
> To: <bioconductor@stat.math.ethz.ch>
>
>
> Hi,
>
> R v 2.0.1 and Limma v 1.8.15
>
> Can anyone please explain to me why I get this error when trying to
use
> the background correct method normexp. I have no missing values and
as
> far as I can tell from looking at summary information this array is
not
> very different from all the others. Other backgroundCorrect methods
work
> fine.
> Code with error is below.
> Thanks,
>
> Helen
>
> library(limma)
> targets=readTargets()
> myfun=function(x) as.numeric(x$Flags>1)
> RG=read.maimages(targets$FileName, source="genepix", wt.fun=myfun)
> RG$printer=getLayout(RG$genes)
> RG$genes=readGAL("M15k4.gal")
> spottypes=readSpotTypes()
> RG$genes$Status=controlStatus(spottypes, RG)
> RGnormexp=backgroundCorrect(RG, method="normexp", offset=50)
> Corrected array 1
> Corrected array 2
> Corrected array 3
> Error in fit.normexp(foreground = RG$G[, j], background = RG$Gb[,
j]) :
> optim failure: degeneracy of the Nelder-Mead simplex
This is a failure in the iterative algorithm used to estimate the
background correction. The
other background correction methods are not iterative. Sorry I don't
have a solution at this
time. We'll continue to work on it to make the estimation algorithm
more bullet-proof.
Gordon
