H Abhilash,

this problem should go away once you upgrade to R 2.8.0 and limma 2.15.10.

Check out these threads with Gordon's explanation of the problem:

http://article.gmane.org/gmane.science.biology.informatics.conductor/18934/match=normexp+limma

You should be able to get the pre-release of R 2.8.0 in this link:
http://mirrors.ibiblio.org/pub/mirrors/CRAN/bin/windows/base/rtest.html

Cheers,
Artur Veloso

On Tue, Sep 30, 2008 at 11:43 AM, Abhilash Venu <abhivenu@gmail.com> wrote:

> Hi all,
>
> I was trying background correction for array CGH data using snapCGH. While
> performing the backgroundCorrection using normexp, which has given me the
> the following error. Could you suggest some solution.
>
> >RG1<-read.maimages("test1.txt",source="agilent")
>
> > RG2 <- backgroundCorrect(RG1, method = "normexp")
>
> Green channel
>
> Corrected array 1
>
> Red channel
>
> Error in if (all(abs(delta) < 1e-10)) break :
>
> missing value where TRUE/FALSE needed
>
> In addition: Warning messages:
>
> 1: In log(1 - alpha * theta) : NaNs produced
>
> 2: In log(1 - alpha * theta) : NaNs produced
>
>
>  sessionInfo()
>
> R version 2.7.0 (2008-04-22)
>
> i386-pc-mingw32
>
>
>  locale:
>
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
> States.1252;LC_MONETARY=English_United
> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
>
>  attached base packages:
>
> [1] splines grid tools stats graphics grDevices utils datasets methods base
>
>
>  other attached packages:
>
> [1] snapCGH_1.8.0 aCGH_1.14.0 sma_0.5.15 multtest_1.16.1 cluster_1.11.10
>
> [6] GLAD_1.16.0 DNAcopy_1.14.0 tilingArray_1.18.0 pixmap_0.4-9
> geneplotter_1.18.0
>
> [11] annotate_1.18.0 xtable_1.5-2 AnnotationDbi_1.2.1 RSQLite_0.6-8
> DBI_0.2-4
>
> [16] genefilter_1.20.0 survival_2.34-1 vsn_3.6.0 lattice_0.17-6
> strucchange_1.3-3
>
> [21] sandwich_2.1-0 zoo_1.5-4 RColorBrewer_1.0-2 affy_1.18.1
> preprocessCore_1.2.0
>
> [26] affyio_1.8.0 Biobase_2.0.1 limma_2.14.3
>
>
>  loaded via a namespace (and not attached):
>
> [1] KernSmooth_2.22-22
>
> Thanks in advance
> --
>
> Regards,
> Abhilash
>
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>
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