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.lalo...@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-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.
