Re: [aroma.affymetrix] Hypersegmentation from "Paired total copy-number analysis" using CRMAv2 with GWSNP6
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 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-8LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8LC_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_2.3.0R.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_0.6.4DNAcopy_1.34.0 PSCBS_0.40.2 > [5] R.cache_0.9.0 R.huge_0.6.0R.rsp_0.9.28tools_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.
Re: [aroma.affymetrix] Hypersegmentation from "Paired total copy-number analysis" using CRMAv2 with GWSNP6
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 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-8LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8LC_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_2.3.0R.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_0.6.4DNAcopy_1.34.0 PSCBS_0.40.2 > > [5] R.cache_0.9.0 R.huge_0.6.0R.rsp_0.9.28tools_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 m
Re: [aroma.affymetrix] Hypersegmentation from "Paired total copy-number analysis" using CRMAv2 with GWSNP6
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 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 > 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 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-8LC_COLLATE=en_US.UTF-8 >> > [5] LC_MONETARY=en_US.UTF-8LC_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_2.3.0R.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_0.6.4DNAcopy_1.34.0 PSCBS_0.40.2 >> > [5] R.cache_0.9.0 R.huge_0.6.0R.rsp_0.9.28tools_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(), an
