Hi Hendrik, Venkat,
we're about to start a large processing run (>20k Affy arrays from GEO,
various platforms). Good time to review/update our old pipeline ...
What is the best way/recomm. parameters now for the min.width argument, and
has the cbs part been modified? Any recommendation to do platform specific
adjustements (majority are 250k & SNP6)?
Pointers appreciated!
Thanks & best,
Michael.
On Wednesday, October 27, 2010 at 9:19:24 PM UTC+2, Venkat wrote:
>
> 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.b...@aroma-project.org <javascript:>> 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 <wang...@gmail.com <javascript:>>
>> 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
>> >>
>> >> >>> > --
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