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 <javascript:> > > 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<javascript:> >> 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 <javascript:>. >> 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.
