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 [[alternative HTML version deleted]]

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/1 8934/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.htm l 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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]