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.
>>
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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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