This can happen occasionally. The min.width argument specifies the minimum
number of probes in the minor arc of the circular (remember this is circular
binary segmentation). So if you can get 2 probes from one end and 3 from
the other to be significantly different the middle you will get a
significant result and a segmentation. I need to change the code in order
to eliminate this possibility.
Venkat
On Wed, Oct 27, 2010 at 2:32 PM, Henrik Bengtsson <
henrik.bengts...@aroma-project.org> wrote:
> 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
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> >>
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> >> >> --
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> >>
> >
> > --
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> >
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> --
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