error in runBioHMM() (package snapCGH)
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@wolfgang-raffelsberger-1805
Last seen 8.0 years ago
Dear list, when analyzing Agilent 44k (human) CGH data* *using the function runBioHMM() from the library snapCGH I've run into an error message described below. Curiously this error has never occurred before although I've been using more or less the same code with previous data-sets where the code was working well ! So I wonder if there's something special with may data, but I can't find any particular anomalies in the data$M.observed (eg I've checked that there are no NAs ...) A summary of the data didn't indicate anything "completely" different to the other arrays, at least nothing that gave the impression beyond those differences due to the nature/biology of the biospies. If you would like to get a copy of the real data, pls let me know, of course the file-size would be way to large for attaching to this message. As the function runBioHMM() doesn't contain a line containing "if ((phi[3, t - 1] + max(-1e+05, log(BFGS.trans.mat[ ..." I'm stuck to get some clues of what may have caused the problem. Note that other segmentation functions form the same package like runDNAcopy() or runGALD() did work without problems !! I'm running code like : library(limma); library(snapCGH); library(DNAcopy); library(GLAD); library(smoothseg) RG1 <- read.maimages(file=mySamples,columns=extrCols1,other.columns= extrOtherCols,source = "agilent") MA1 <- normalizeBetweenArrays(RG1,method="Aquantile") MA1$design <- rep(-1,ncol(MA1$M)) MA1_snpCGH <- processCGH(MA1, maxChromThreshold = length(na.omit(unique(MA1$genes$Chr))) ) MA1_snpCGH$genes$Position <- round(MA1_snpCGH$genes$Position,6) # transform to Mb scale ## checking (some of) my data summary( MAagil_snpCGH$M.observed[,155:156] ) ## gives : M.111_CN_18 M.111_CN_19 Min. :-4.856865 Min. :-2.919297 1st Qu.:-0.243359 1st Qu.:-0.235424 Median :-0.044505 Median :-0.039601 Mean : 0.007306 Mean : 0.001244 3rd Qu.: 0.163834 3rd Qu.: 0.152406 Max. : 7.773869 Max. : 4.161682 MA1_snpCGH$M <- MA1_snpCGH$M.observed ## and here I (consitently) get the error : (message truncated to show the end) sample is 153 Chromosomes: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 sample is 154 Chromosomes: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 sample is 155 Chromosomes: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 sample is 156 Chromosomes: 1 2 3 4 5 6 7 8 9 10 11 Error in if ((phi[3, t - 1] + max(-1e+05, log(BFGS.trans.mat[[t - 1]][3, : missing value where TRUE/FALSE needed In addition: There were 50 or more warnings (use warnings() to see the first 50) Error in res$nstates.list : $ operator is invalid for atomic vectors ## for completeness: > sessionInfo() R version 2.8.0 (2008-10-20) x86_64-unknown-linux-gnu locale: C attached base packages: [1] splines grid tools stats graphics grDevices utils [8] datasets methods base other attached packages: [1] smoothseg_0.0.1 OCplus_1.16.0 akima_0.5-1 [4] snapCGH_1.10.0 aCGH_1.16.0 sma_0.5.15 [7] multtest_1.22.0 cluster_1.11.11 GLAD_1.18.0 [10] DNAcopy_1.16.0 tilingArray_1.20.0 pixmap_0.4-9 [13] geneplotter_1.20.0 annotate_1.20.1 xtable_1.5-4 [16] AnnotationDbi_1.4.1 genefilter_1.22.0 survival_2.34-1 [19] vsn_3.8.0 lattice_0.17-15 strucchange_1.3-4 [22] sandwich_2.1-0 zoo_1.5-4 RColorBrewer_1.0-2 [25] affy_1.20.0 Biobase_2.2.1 limma_2.16.3 loaded via a namespace (and not attached): [1] DBI_0.2-4 KernSmooth_2.22-22 RSQLite_0.7-1 [4] affyio_1.10.1 preprocessCore_1.4.0 Any suggestions how to resolve this problem would be very much appreciated ! Wolfgang Raffelsberger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Wolfgang Raffelsberger, PhD Laboratoire de BioInformatique et G?nomique Int?gratives CNRS UMR7104, IGBMC, 1 rue Laurent Fries, 67404 Illkirch Strasbourg, France Tel (+33) 388 65 3300 Fax (+33) 388 65 3276 wolfgang.raffelsberger (at) igbmc.fr
CGH snapCGH CGH snapCGH • 571 views
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