This doesn't sound good. It makes Oncoscan unusable for research projects. Michael.
> On 11 Nov 2015, at 23:40, Keith C <keithchi...@gmail.com> wrote: > > 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/ > <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.
