snapCGH_error in plotting segmentation
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Abhilash Venu ▴ 340
@abhilash-venu-2680
Last seen 10.2 years ago
Hi all, I was performing analysis on X chromosome tiling array using snapCGH. when I have used the 'plotSegmentedGenome(SegInfo.Hom.merged, array = 1)', I got the following error "Error in xlim[2] <- clone.genomepos[sum(clone.genomepos > 0)] : nothing to replace with" . I am wondering how could I overcome this proble. Thanks in advance -- Regards, Abhilash [[alternative HTML version deleted]]
snapCGH snapCGH • 1.3k views
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@sean-davis-490
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On Tue, Sep 23, 2008 at 12:14 PM, Abhilash Venu <abhivenu at="" gmail.com=""> wrote: > Hi all, > > I was performing analysis on X chromosome tiling array using snapCGH. when I > have used the 'plotSegmentedGenome(SegInfo.Hom.merged, array = 1)', I got > the following error "Error in xlim[2] <- clone.genomepos[sum(clone.genomepos >> 0)] : nothing to replace with" . I am wondering how could I overcome this > proble. Hi, Abhilash. You'll need to post the code you have used and sessionInfo() for all questions to the list. Otherwise, it is quite difficult to help. Sean
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Hi Sean As you directed, I am sending the script and few lines of the data which I am reading from the agilent txt file. The following is the data. ID Chr Genename Description Position gMeanSignal rMeanSignal gBGMeanSignal rBGMeanSignal 1 23 chrX:43061775-43061835 Unknown 43061775 2.769435e+003 7.962903e+001 1.319006e+003 4.802372e+001 2 23 CUL4B ref|Homo sapiens cullin 4B (CUL4B), transcript variant 2, mRNA. 119544771 2.838167e+003 7.663333e+001 1.336585e+003 4.839526e+001 3 23 chrX:128116561-128116621 Unknown 128116561 3.050850e+003 7.963333e+001 1.321223e+003 4.746215e+001 #Reading the above data (244K, Agilent) >RG1=read.maimages("test1.txt",columns=list(G="gMeanSignal",Gb="gBGMea nSignal", R="rMeanSignal",Rb="gBGMeanSignal"), annotation=c("ID","Chr","Position","Name")) >RG1$design <- c(1) #only one array > RG2 <- backgroundCorrect(RG1, method = "minimum") > MA <- normalizeWithinArrays(RG2, method = "median") >MA2 <- processCGH(MA, method.of.averaging = mean, ID = "ID") # when I applied this I got thefollowing error message "Error in processCGH(MA, method.of.averaging = mean, ID = "ID") : object "segList" not found". But this I overcome by applying following command befor using "processCGH". >segList <- list() segList$M.observed <- MA$M segList$genes <- MA$genes # after this I used the processCGH, this could eliminate the error. Could you comment on this? >SegInfo.Hom <- runHomHMM(MA2, criteria = "AIC") >SegInfo.Hom.merged <- mergeStates(SegInfo.Hom, MergeType = 1) >plotSegmentedGenome(SegInfo.Hom.merged, array = 1) Error in xlim[2] <- clone.genomepos[sum(clone.genomepos > 0)] : nothing to replace with The above was the script, this is as per the tutorial. Could you help me to overcome this? Thanks in advance. Abhilash On Tue, Sep 23, 2008 at 11:01 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Tue, Sep 23, 2008 at 12:14 PM, Abhilash Venu <abhivenu@gmail.com> > wrote: > > Hi all, > > > > I was performing analysis on X chromosome tiling array using snapCGH. > when I > > have used the 'plotSegmentedGenome(SegInfo.Hom.merged, array = 1)', I got > > the following error "Error in xlim[2] <- > clone.genomepos[sum(clone.genomepos > >> 0)] : nothing to replace with" . I am wondering how could I overcome > this > > proble. > > Hi, Abhilash. You'll need to post the code you have used and > sessionInfo() for all questions to the list. Otherwise, it is quite > difficult to help. > > Sean > -- Regards, Abhilash [[alternative HTML version deleted]]
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On Wed, Sep 24, 2008 at 11:48 AM, Abhilash Venu <abhivenu at="" gmail.com=""> wrote: > Hi Sean > As you directed, I am sending the script and few lines of the data which I > am reading from the agilent txt file. The following is the data. > ID Chr Genename Description Position gMeanSignal > rMeanSignal gBGMeanSignal rBGMeanSignal > 1 23 chrX:43061775-43061835 Unknown 43061775 2.769435e+003 > 7.962903e+001 1.319006e+003 4.802372e+001 > 2 23 CUL4B ref|Homo sapiens cullin 4B (CUL4B), transcript variant > 2, mRNA. 119544771 2.838167e+003 7.663333e+001 1.336585e+003 > 4.839526e+001 > 3 23 chrX:128116561-128116621 Unknown 128116561 > 3.050850e+003 7.963333e+001 1.321223e+003 4.746215e+001 > > #Reading the above data (244K, Agilent) > >>RG1=read.maimages("test1.txt",columns=list(G="gMeanSignal",Gb="gBGMe anSignal", > > R="rMeanSignal",Rb="gBGMeanSignal"), > > annotation=c("ID","Chr","Position","Name")) > >>RG1$design <- c(1) #only one array > >> RG2 <- backgroundCorrect(RG1, method = "minimum") > >> MA <- normalizeWithinArrays(RG2, method = "median") > >>MA2 <- processCGH(MA, method.of.averaging = mean, ID = "ID") # when I >> applied this I got thefollowing error message "Error in processCGH(MA, >> method.of.averaging = mean, ID = "ID") : object "segList" not found". But >> this I overcome by applying following command befor using "processCGH". > >>segList <- list() > > segList$M.observed <- MA$M > > segList$genes <- MA$genes # after this I used the processCGH, this > could eliminate the error. Could you comment on this? > >>SegInfo.Hom <- runHomHMM(MA2, criteria = "AIC") > >>SegInfo.Hom.merged <- mergeStates(SegInfo.Hom, MergeType = 1) > >>plotSegmentedGenome(SegInfo.Hom.merged, array = 1) > > Error in xlim[2] <- clone.genomepos[sum(clone.genomepos > 0)] : > > nothing to replace with > > The above was the script, this is as per the tutorial. Could you help me to > overcome this? And your sessionInfo()? Sean > On Tue, Sep 23, 2008 at 11:01 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >> >> On Tue, Sep 23, 2008 at 12:14 PM, Abhilash Venu <abhivenu at="" gmail.com=""> >> wrote: >> > Hi all, >> > >> > I was performing analysis on X chromosome tiling array using snapCGH. >> > when I >> > have used the 'plotSegmentedGenome(SegInfo.Hom.merged, array = 1)', I >> > got >> > the following error "Error in xlim[2] <- >> > clone.genomepos[sum(clone.genomepos >> >> 0)] : nothing to replace with" . I am wondering how could I overcome >> >> this >> > proble. >> >> Hi, Abhilash. You'll need to post the code you have used and >> sessionInfo() for all questions to the list. Otherwise, it is quite >> difficult to help. >> >> Sean > > > > -- > > Regards, > Abhilash >
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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 On Wed, Sep 24, 2008 at 9:23 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Wed, Sep 24, 2008 at 11:48 AM, Abhilash Venu <abhivenu@gmail.com> > wrote: > > Hi Sean > > As you directed, I am sending the script and few lines of the data which > I > > am reading from the agilent txt file. The following is the data. > > ID Chr Genename Description Position gMeanSignal > > rMeanSignal gBGMeanSignal rBGMeanSignal > > 1 23 chrX:43061775-43061835 Unknown 43061775 2.769435e+003 > > 7.962903e+001 1.319006e+003 4.802372e+001 > > 2 23 CUL4B ref|Homo sapiens cullin 4B (CUL4B), transcript > variant > > 2, mRNA. 119544771 2.838167e+003 7.663333e+001 1.336585e+003 > > 4.839526e+001 > > 3 23 chrX:128116561-128116621 Unknown 128116561 > > 3.050850e+003 7.963333e+001 1.321223e+003 4.746215e+001 > > > > #Reading the above data (244K, Agilent) > > > > >>RG1=read.maimages("test1.txt",columns=list(G="gMeanSignal",Gb="gBG MeanSignal", > > > > R="rMeanSignal",Rb="gBGMeanSignal"), > > > > annotation=c("ID","Chr","Position","Name")) > > > >>RG1$design <- c(1) #only one array > > > >> RG2 <- backgroundCorrect(RG1, method = "minimum") > > > >> MA <- normalizeWithinArrays(RG2, method = "median") > > > >>MA2 <- processCGH(MA, method.of.averaging = mean, ID = "ID") # when I > >> applied this I got thefollowing error message "Error in processCGH(MA, > >> method.of.averaging = mean, ID = "ID") : object "segList" not found". > But > >> this I overcome by applying following command befor using "processCGH". > > > >>segList <- list() > > > > segList$M.observed <- MA$M > > > > segList$genes <- MA$genes # after this I used the processCGH, > this > > could eliminate the error. Could you comment on this? > > > >>SegInfo.Hom <- runHomHMM(MA2, criteria = "AIC") > > > >>SegInfo.Hom.merged <- mergeStates(SegInfo.Hom, MergeType = 1) > > > >>plotSegmentedGenome(SegInfo.Hom.merged, array = 1) > > > > Error in xlim[2] <- clone.genomepos[sum(clone.genomepos > 0)] : > > > > nothing to replace with > > > > The above was the script, this is as per the tutorial. Could you help me > to > > overcome this? > > And your sessionInfo()? > > Sean > > > On Tue, Sep 23, 2008 at 11:01 PM, Sean Davis <sdavis2@mail.nih.gov> > wrote: > >> > >> On Tue, Sep 23, 2008 at 12:14 PM, Abhilash Venu <abhivenu@gmail.com> > >> wrote: > >> > Hi all, > >> > > >> > I was performing analysis on X chromosome tiling array using snapCGH. > >> > when I > >> > have used the 'plotSegmentedGenome(SegInfo.Hom.merged, array = 1)', I > >> > got > >> > the following error "Error in xlim[2] <- > >> > clone.genomepos[sum(clone.genomepos > >> >> 0)] : nothing to replace with" . I am wondering how could I overcome > >> >> this > >> > proble. > >> > >> Hi, Abhilash. You'll need to post the code you have used and > >> sessionInfo() for all questions to the list. Otherwise, it is quite > >> difficult to help. > >> > >> Sean > > > > > > > > -- > > > > Regards, > > Abhilash > > > -- Regards, Abhilash [[alternative HTML version deleted]]
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