>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 
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