Affy recommended to use Nexus software. To generate CNV plots, I used the probe level output from Nexus.
-keith On Mon, Jul 10, 2017 at 6:21 AM, Francesca Scellato < francesca.scell...@gmail.com> wrote: > Hi! > I found online this discussion because I'm looking for the CDF file for > Oncoscan CNV array. > I'm new to R and data analysis but everything that I've found so far to > analyze CEL files requires that CDF file. > > Have you managed to find a solution during these past years? > > Thank you in advance. > > Il giorno sabato 14 novembre 2015 00:15:03 UTC+1, Henrik Bengtsson ha > scritto: >> >> Ok, so that complicates how one would look at the pre-processing and >> how to normalize the signals, e.g. one should probably normalize probe >> signals of the two CEL files separately and only merge them after this >> step. >> >> A small first step would be to see if you can create a spatial image >> of the CEL files, e.g. >> >> library("aroma.affymetrix") >> df <- AffymetrixCelFile("rawData/FusionSDK_Test3/Test3/Test3-1-121502.CEL") >> >> print(df) >> >> ## Display in R >> img <- getImage(df) >> display(img) >> >> ## Generate a PNG and view it >> png <- writeImage(df) >> browseURL(png) >> >> /Henrik >> >> >> On Thu, Nov 12, 2015 at 5:05 PM, Keith C <keith...@gmail.com> wrote: >> > the CEL files are generated from two separate chips and hybs. >> > >> > -- >> > -- >> > 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/f >> orum/ >> > >> > --- >> > 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/d/optout. >> > -- > -- > 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 a topic in the > Google Groups "aroma.affymetrix" group. > To unsubscribe from this topic, visit https://groups.google.com/d/ > topic/aroma-affymetrix/Wez3wL1abiA/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit https://groups.google.com/d/optout. > -- -- 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/d/optout.