Hi, I've bbc:ed Venkat since I don't know if he's on this list or not.
I don't have any particular suggestions for tweaking the default DNAcopy::segment() CBS parameters. If you missed it, both aroma.affymetrix and PSCBS now supports parallel process to some extent, cf. http://www.aroma-project.org/howtos/parallel_processing/ /Henrik On Tue, Feb 2, 2016 at 6:28 AM, mbaudis <mbau...@gmail.com> wrote: > 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> 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> 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 >>> >> >>> > 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-af...@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 >>> >> >> websitehttp://www.aroma-project.org/. >>> >> >> To post to this group, send email to aroma-af...@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-af...@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-af...@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/ > > --- > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. -- -- 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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