Are you sure you are not picking up old results, that is, did you use
fit(cbs, ..., force=TRUE) or simply did you remove the previous
segmentation results in cbsData/?
You can troubleshoot with one array and one chromosome, e.g.
fit(cbs, arrays=6, chromosomes=16, min.width=5, undo.splits="sdundo",
undo.SD=1, force=TRUE, verbose=-10);
/Henrik
On Wed, Oct 27, 2010 at 11:20 AM, Kai <wangz...@gmail.com> wrote:
> Hi Henrik,
>
> Thank you for your reply. However, I followed your instructions but
> still got segments with only 2 markers:
>
> These are the codes I ran:
>
> cbs = CbsModel(ds);
> cbs$.calculateRatios = FALSE;
> fit(cbs, chromosomes=c(1:23), min.width=5, undo.splits="sdundo",
> undo.SD=1, verbose=-10);
> ce = ChromosomeExplorer(cbs);
> process(ce,chromosomes=c(1:23));
>
> These are what I found out in the results (there are a total of 4
> samples):
>
>> min(getRegions(cbs)[[1]][,5])
> [1] 5
>> min(getRegions(cbs)[[2]][,5])
> [1] 2
>> min(getRegions(cbs)[[3]][,5])
> [1] 2
>> min(getRegions(cbs)[[4]][,5])
> [1] 2
>> which(getRegions(cbs)[[4]][,5]==2)
> [1] 52 139
>> getRegions(cbs)[[4]][139,1:5]
> chromosome start stop mean count
> 139 16 45057510 45057696 -1.427 2
>
> It seems to me that min.width=5 worked only in the first sample. Do
> you have any idea on this? Thanks!
>
> Best,
> Kai
>
>
> On Oct 26, 9:09 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> I forgot to say that in the next release of aroma.core package, you
>> will be able to specify additional arguments when you setup the CBS
>> model:
>>
>> cbs <- CbsModel(ds, min.width=5);
>>
>> ...but until then you have to stick with the below workaround.
>>
>> /Henrik
>>
>> On Tue, Oct 26, 2010 at 9:07 PM, hb <h...@biostat.ucsf.edu> wrote:
>> > Hi,
>>
>> > sorry my mistake. I meant to write that you should pass the additional
>> > arguments to fit() for the CbsModel (not process()), e.g.
>>
>> > cbs <- CbsModel(ds);
>> > cbs$.calculateRatios <- FALSE;
>> > fit(cbs, chromosomes=1:23, min.width=5, verbose=-10);
>>
>> > This will (explicitly) fit the segmentation model. Have a look at the
>> > verbose output; you'll see that "min.width" should show up in the output
>> > just before the DNAcopy segment() is called.
>>
>> > After you've done the segmentation for all of you arrays and chromosomes,
>> > you can have the ChromosomeExplorer generate the report for you as usual,
>> > i.e.
>>
>> > ce <- ChromosomeExplorer(cbs);
>> > process(ce, chromosomes=1:23);
>>
>> > Note that in your case you have to either delete already generated CBS
>> > results, or use fit(..., force=TRUE), in order for aroma.* not to pick up
>> > the old segmentation. You also need to delete the already generated PNG
>> > files for the ChromosomeExplorer under reports/...
>>
>> > On Tue, Oct 26, 2010 at 4:43 PM, Kai <wangz...@gmail.com> wrote:
>> >> Hi Henrik,
>>
>> >> Thank you very much for your response. However, I tried the following
>> >> codes to set the minimal number of marker to 5, but the results I got
>> >> still contain segments with only 2 markers ...
>>
>> >> cbs = CbsModel(ds);
>> >> cbs$.calculateRatios = FALSE;
>> >> ce = ChromosomeExplorer(cbs);
>> >> process(ce,chromosomes=c(1:23),min.width=5);
>>
>> >> I am not clear where I should put "min.width=5"? If I do
>> >> "process(cbs,min.width=5)" first, how can I send the results to be
>> >> displayed by chromosome explorer?
>>
>> >> Thanks again for your help. I look forward to hearing from you soon.
>>
>> >> Best,
>> >> Kai
>>
>> >> On Sep 27, 9:47 pm, Henrik Bengtsson <henrik.bengts...@gmail.com>
>> >> wrote:
>> >>> Hi.
>>
>> >>> On Mon, Sep 27, 2010 at 4:51 PM, Kai <wangz...@gmail.com> wrote:
>> >>> > Hi Henrik,
>>
>> >>> > I was wondering whether there is a way I can fine tune the behavior of
>> >>> > CbsModel. Sometimes the default algorithm produces too many small
>> >>> > fragments right next to each other without much separation in mean
>> >>> > copy numbers. Is there a way to control how "smooth" the segmentation
>> >>> > results are?
>>
>> >>> Any additional arguments (in "...") that you pass to process(cbs, ...)
>> >>> will be passed down to the DNAcopy::segment(), which is the function
>> >>> doing the actual segmentation. For more details on how fine tuning
>> >>> the CBS algorithm, see help("segment", package="DNAcopy"). You may
>> >>> also want to contact the authors of that method/package.
>>
>> >>> /Henrik
>>
>> >>> > Thanks a lot!
>>
>> >>> > Best,
>> >>> > Kai
>>
>> >>> > --
>> >>> > When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >>> > latest
>> >>> > version of the package, 2) to report the output of sessionInfo() and
>> >>> > traceback(), and 3) to post a complete code example.
>>
>> >>> > You received this message because you are subscribed to the Google
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>> >>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>> >>> > To unsubscribe and other options, go
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>>
>> >> --
>> >> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> >> latest version of the package, 2) to report the output of sessionInfo()
>> >> and traceback(), and 3) to post a complete code example.
>>
>> >> You received this message because you are subscribed to the Google Groups
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>>
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
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