[BioC] snapCGH_error in plotting segmentation
sdavis2 at mail.nih.gov
Wed Sep 24 17:53:52 CEST 2008
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
> 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$design <- c(1) #only one array
>> RG2 <- backgroundCorrect(RG1, method = "minimum")
>> MA <- normalizeWithinArrays(RG2, method = "median")
>>MA2 <- processCGH(MA, method.of.averaging = mean, ID = "ID") # when I
>> applied this I got thefollowing error message "Error in processCGH(MA,
>> method.of.averaging = mean, ID = "ID") : object "segList" not found". But
>> this I overcome by applying following command befor using "processCGH".
>>segList <- list()
> segList$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 <- 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()?
> 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>
>> > 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 <-
>> > 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.
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