Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files

Thank you all for your answers. I was able to export from Nexus the segment, probes and snps file for each sample. I'm still looking for an alternative way to process the CEL files (other that Nexus) that will allow a more personalized analysis; I've come across the Affymetrix Power Tools but I

Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files

its actually under Convert.. From: Andrea O'Hara Date: Thursday, November 12, 2015 11:35 AM To: Keith Ching , "Foos, Jonathon" < jonathon_f...@affymetrix.com> Subject: RE: Affymetrix Oncoscan bioinformatics - follow up 1. Hi Keith, Thank you

Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files

Nexus outputs the probe positions and intensities as well as the segmentation data. Just export it as text tables if you want to mine the whole data. Agreed, looking at one gene at a time is a waste. But now you need to figure out how to do it for 50K arrays since, inexplicably, you have to

Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files

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

Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files

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.

Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files

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

Re: [aroma.affymetrix] Re: Affymetrix Oncoscan library files

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