[BioC] snapCGH_error in plotting segmentation

[Sean Davis]

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="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 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
>