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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> >> To post to this group, send email to aroma-affymetrix@googlegroups.com
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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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