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 Groups
>>> > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/.
>>> > To post to this group, send email to aroma-affymetrix@googlegroups.com
>>> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/
>>>
>>>
>>
>> --
>> 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
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to aroma-affymetrix@googlegroups.com
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>
>
--
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
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
