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. Best, Pierre On Wed, Dec 4, 2013 at 5:29 PM, Emilie <emilie.lalo...@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-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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