  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?

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

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