Hi, sorry for the delay. The problem with hyper-segmentation is really an issue post CRMAv2 preprocessing. By the "broadinstitute copy number pipeline", do you mean
http://www.broadinstitute.org/cancer/software/genepattern/modules/snp6copynumberpipeline If so, then they're doing two things before CBS; (i) removing outliers and (ii) "tangent" normalization toward a normal reference set. The latter is not implemented in the Aroma Framework and I don't know of another implementation in R/Bioconductor either (but it may exist). Removing outliers before calling CBS is not implemented in the Aroma Framework, but can be done using the PSCBS package [http://cran.r-project.org/web/packages/PSCBS]. I've recently commented on how to use the PSCBS package for this, cf. thread 'smoothing after CRMAv2 and before CBS?' on 2013-12-17 [https://groups.google.com/d/msg/aroma-affymetrix/DUquhAMhEuY/J6lqIgozK2YJ]. That thread also show how to do post CBS/PSCBS pruning using the pruneByHClust(), which is also illustrated in the PSCBS package vignettes. Hope this helps Henrik On Tue, Dec 17, 2013 at 9:55 PM, Hoon Kim <wise...@gmail.com> wrote: > Dear Henrik, > > I am very sorry for having not provided details before. > What I wanted to address was if there would be a way (such as controlling > CBS parameters) to eliminate hyper-segmentations using CRMAv2. > I think this issue is NOT related to a new version of CRMAv2 but is specific > to my current affymetrix data. > The broadinstitute copy number pipeline performs several preprocessing > before finally applying CBS for segmentation. > But, this does not support paired analysis, which is one of the main reasons > why I prefer aroma.affymetrix. > > The top panel in the figure represents IGV view of the CRMV2-based segmented > copy numbers, while the bottom panel is an IGV view of the broadinstitute > pipeline-based copy numbers. In both panels, red represents strength of > amplification, while blue represents strength of deletion. > > I would appreciate it if you give some advice on how to reduce such > hyper-segmentation using CRMAv2, if any, according to your experience. > > best, > > Kim > > > > > > On Tue, Dec 17, 2013 at 11:37 PM, Henrik Bengtsson > <henrik.bengts...@aroma-project.org> wrote: >> >> Hi. >> >> 1. It is not clear to me if you're saying that you get different >> results now using a newer version of aroma.affymetrix that you used >> before and on the same exact same data set, or something else. >> Nothing intentionally have changed in the CRMAv2 pipeline (and I >> cannot recall any recent updates at all to that pipeline), so if it >> "recently" started to "fail", it is most likely your data that is >> different now than what you used before. >> >> 2. It is not clear to me if you used CRMAv2 data for the "broad >> institute pipeline" or if that is a completely different pipeline. I >> also don't know what "broad institute pipeline" is. Is it using CBS >> for segmentation, or something else etc etc. >> >> 3. I don't know what I'm looking at in Picture1.png. >> >> /Henrik >> >> >> On Tue, Dec 17, 2013 at 8:47 PM, wisekh6 <wise...@gmail.com> wrote: >> > Dear Henrik, >> > >> > I had been using CRMAv2 many times to generate segmented copy numbers >> > from >> > "Paired total copy-number analysis" using CRMAv2 with affymetrix snp6, >> > and >> > all of my trials were successful. >> > Recently, however, this approach failed to generate a reasonable number >> > of >> > segments, while an alternative way (using broad institute pipeline) >> > worked >> > well, as shown in the attached. >> > I wonder if you can have a chance to examine this difference with any >> > intermediate file that CRMAv2 generated. >> > If you let me know which file you need, please let me know. >> > thank you in advance. >> > >> > Kim >> > >> > >> >> sessionInfo() >> > R version 3.0.1 (2013-05-16) >> > Platform: x86_64-unknown-linux-gnu (64-bit) >> > >> > locale: >> > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 >> > [7] LC_PAPER=C LC_NAME=C >> > [9] LC_ADDRESS=C LC_TELEPHONE=C >> > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> > >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods base >> > >> > other attached packages: >> > [1] aroma.light_1.30.5 matrixStats_0.8.12 >> > aroma.affymetrix_2.11.1 >> > [4] affxparser_1.32.3 aroma.core_2.11.0 R.devices_2.7.2 >> > [7] R.filesets_2.3.0 R.utils_1.28.4 R.oo_1.15.8 >> > [10] R.methodsS3_1.5.2 >> > >> > loaded via a namespace (and not attached): >> > [1] aroma.apd_0.4.0 digest_0.6.4 DNAcopy_1.34.0 PSCBS_0.40.2 >> > [5] R.cache_0.9.0 R.huge_0.6.0 R.rsp_0.9.28 tools_3.0.1 >> > >> > -- >> > -- >> > 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/groups/opt_out. >> >> -- >> -- >> 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/groups/opt_out. > > > -- > -- > 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/groups/opt_out. -- -- 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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