The tumor DH panel makes me believe that either your tumor or your normal chip data is bad, or alternatively that the tumor and normal are not matched.
Check the allele B fraction of your normal. It should show three distinct bands. Do the same for the tumor. It should also show distinct bands with varying of bands depending on aberrations. If both look clean, then it's likely they're not matched. If one is very noisy, then that one is simply a bad run/sample. Henrik On Dec 12, 2013 12:42 PM, "Emilie" <emilie.lalo...@gmail.com> wrote: > Thank you both very much! I was indeed referring to smooth.cna, sorry > about that confusion. > > I've switched over to PSCBS and used the dropSegmentationOutliers- it > seems to be running well. I've noticed that some of my samples have very > fragmented profiles (see attached). Does this suggest poor quality data, or > maybe an error in my normalization/plotting? Not all samples are like this, > but it almost seems like the order of the of the probes is scrambled? > > > Emilie > > > On Thursday, December 5, 2013 1:08:46 PM UTC-5, Henrik Bengtsson wrote: >> >> Pierre beat me to this one. Comments below... >> >> On Thu, Dec 5, 2013 at 9:20 AM, Pierre Neuvial >> <pierre....@genopole.cnrs.fr> wrote: >> > Hi Emilie, >> > >> > OK, so you are referring to the “smooth.CNA" function in the DNAcopy >> > package, cf >> > http://www.bioconductor.org/packages/2.13/bioc/vignettes/ >> DNAcopy/inst/doc/DNAcopy.pdf >> > >> > What this function is doing is detecting outliers (based on how far >> their >> > signal value is from their neighbors) and shrink their signal values >> toward >> > those of their neighbors. >> > >> > This is indeed appropriate and recommended. I thought that by >> "smoothing" >> > you meant performing some kind of local averaging of the original >> signal >> > (e.g. using a mobile median or by binning): this I don't recommend. >> Sorry >> > for the confusion. >> > >> > >> > To drop outliers, one possibility is to use the >> "dropSegmentationOutliers" >> > function from the PSCBS package. See the vignettes at >> > http://cran.fhcrc.org/web/packages/PSCBS/index.html >> > >> > Another comment: since you are following the vignette for paired CNA >> > analysis, I am guessing that you are working with tumor/normal pairs. >> If >> > so, then you should use PSCBS rather than CBS for segmentation. PSCBS >> is an >> > extension of CBS to segment not only total copy numbers but also >> allelic >> > ratios. See the PSCBS vignette in the above URL. >> >> To balance this a little bit, I would say there may exist outliers in >> the total copy number (TCN) signals that are so sever that they bias >> the estimators/test statistic of CBS (which assumes Gaussian signals). >> If one believes there are such outliers and worries that they are so >> extreme that they would affect the segmentation severely, one could >> either (i) drop or (ii) shrink ("smooth") them. In the vignettes of >> the PSCBS package, I've last night [PSCBS (>= 0.39.8)] >> corrected/clarified Section 'Dropping TCN outliers' to say the >> following: >> >> "There may be some outliers among the TCNs. In >> CBS~\citep{OlshenA_etal_2004,VenkatramanOlshen_2007}, the authors >> propose a method for identifying outliers and then to shrink such >> values toward their neighbors ("smooth") before performing >> segmentation. At the time CBS was developed it made sense to not just >> to drop outliers because the resolution was low and every datapoint >> was valuable. With modern technologies the resolution is much higher >> and we can afford dropping such outliers, which can be done by: >> >> > data <- dropSegmentationOutliers(data) >> >> Dropping TCN outliers is optional." >> >> Hope this clarifies. >> >> Back to the original question: It is not possible to drop (or smooth) >> outliers using the CbsModel() pipeline [I'll add that to the todo >> list]. The easiest is to turn use the PSCBS package, where you can do >> plain old single-track CBS segmentation, paired PSCBS segmentation and >> also non-paired PSCBS segmentation. As Pierre says, if you have tumor >> SNP data, you should look into doing parent-specific CN analysis, >> which you can do either via paired or non-paired PSCBS depending on >> whether you have match normals or not. >> >> To take your allele-specific CRMAv2 and bring it into a format >> recognized by the PSCBS package, see >> http://aroma-project.org/vignettes/PairedPSCBS-lowlevel >> >> /Henrik >> >> > >> > Best, >> > >> > Pierre >> > >> > >> > On Wed, Dec 4, 2013 at 5:29 PM, Emilie <emilie....@gmail.com> wrote: >> >> >> >> Hi Pierre, >> >> >> >> Thanks for your answer. I may be wrong but I thought smoothing prior >> to >> >> segmentation was somewhat common. It is shown in the vignettes for >> DNACopy >> >> and seems to be fairly common in the literature (this approach was >> used in >> >> the Metabric paper for example, >> >> http://www.ncbi.nlm.nih.gov/pubmed/22522925). >> >> >> >> I'd be interested in hearing more of your thoughts against this. Do >> you >> >> have an idea of how much resolution is lost by smoothing? >> >> >> >> Emilie >> >> >> >> >> >> >> >> On Tuesday, December 3, 2013 5:26:38 PM UTC-5, Pierre Neuvial wrote: >> >>> >> >>> Hi Emilie, >> >>> >> >>> It's certainly possible to do this within the Aroma framework (e.g. >> using >> >>> the function "binnedSmoothing"). It's probably not as >> straightforward as >> >>> running the segmentation directly, though, because this is not a >> typical use >> >>> case. >> >>> >> >>> In fact, I'm not sure why you want to perform smoothing before >> >>> segmentation ? Smoothing is definitely not required before >> segmentation, >> >>> and I would actually discourage to go this path because it will end >> up in a >> >>> loss of resolution along the genome at the smoothing step. >> >>> >> >>> Best, >> >>> >> >>> Pierre >> >>> >> >>> >> >>> On Tue, Dec 3, 2013 at 8:53 PM, Emilie <emilie....@gmail.com> wrote: >> >>>> >> >>>> Hi there, >> >>>> >> >>>> I'm new to processing Affy SNP6 chips and so am mainly experimenting >> >>>> with different methods to date. I ran CRMAv2 and followed steps 1-4 >> from the >> >>>> vignette (http://aroma-project.org/vignettes/CRMAv2). For step 5, I >> want to >> >>>> do a paired analysis. >> >>>> >> >>>> Previously I've used DNAcopy to perform CBS for other array types, >> and >> >>>> would like to follow a similar procedure, which includes smoothing >> prior to >> >>>> segmentation. Is this possible using the aroma.affymetrix package? >> So far >> >>>> I've followed the vignette for paired CNA analysis >> >>>> (http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis) >> but >> >>>> haven't seen any options for smoothing. >> >>>> >> >>>> thank you very much, >> >>>> >> >>>> emilie >> >>>> >> >>>> -- >> >>>> -- >> >>>> 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/ >> >>>> >> >>>> --- >> >>>> 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-affymetr...@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-af...@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-affymetr...@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-af...@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-affymetr...@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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