>From what I understand, the OncoScan assay has a different capture method but in the end still involves hybridization to probes on a chip. The output is two CEL files, A and C which represent AT and GC. Using their oncoscan software, it combines the two CEL files into a .OSCHP file which you can process with DNA Nexus. One advantage is that they have precharacterized normal diploid cells so that a hapmap reference sample is no longer required. However, the process is a pain and involves a lot of manual interface clicking, file matching, and manual generation of images. I have not found a way to simply export the segmentation data. I was told by Affy that OncoScan does not use a CDF file, but rather a PGR.CLF file. I'm trying to get a hold of one to see what the difference is and if its convertable into CDF format.
What I mainly want is a chromosome explorer type output of 1. images of all chromosomes for all samples. (that's 24 plots by hand per sample using Nexus ) 2. segmentation file including non-cnv altered segments. Currently Nexus only outputs regions of significance. -- -- 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 email@example.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.