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="gBGMeanSignal",
> >
> >  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

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