> Affy recommended to use Nexus software. To generate CNV plots, I used the > probe level output from Nexus.
That (generating plots) is not the point; though I am all for nice CNV plots (ahem, arraymap.org <http://arraymap.org/>), these have no use for data mining/meta-analyses etc. I had Affymetrix representatives in my office showing me plots of our Oncoscan data, w/o any idea how to extract probe/segment specific values. And, while conversing with many colleagues, nobody knows, either. So, for us: We're having cancer profiling raw data from a series of rare diseases, which is rotting since we have no way of extracting genome mapped raw intensities / segmentation calls etc. And we're running a resource with >50000 cancer CNA profiles/datasets - but none of them Oncoscan (damned be thy name). Michael. > -keith > > On Mon, Jul 10, 2017 at 6:21 AM, Francesca Scellato > <francesca.scell...@gmail.com <mailto: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/ > > <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/ > > <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/d/optout > > <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/ > <http://www.aroma-project.org/>. > To post to this group, send email to aroma-affymetrix@googlegroups.com > <mailto:aroma-affymetrix@googlegroups.com> > To unsubscribe and other options, go to http://www.aroma-project.org/forum/ > <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 > <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 > <mailto:aroma-affymetrix+unsubscr...@googlegroups.com>. > For more options, visit https://groups.google.com/d/optout > <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/ > <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/ > <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 > <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 > <mailto:aroma-affymetrix+unsubscr...@googlegroups.com>. > For more options, visit https://groups.google.com/d/optout > <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.
