Actually, if there are regular CEL files outputted, and assuming they're not non-supported multi-channel CEL files, then it might not be an impossible task. There is still a need for a CDF though, but people have built CDF for Affymetrix chiptypes that don't official have CDFs.
First question that comes to mind is whether the two CEL files are coming from a single hybridization/chip, or two separate hybridizations/chips. If from a single one, then one could imagine creating a virtual chip where one start by merging the data from the two CEL files into one bigger CEL file. Likewise, one can then create one CDF file for this virtual file. From there, low-level affxparser should be able to parse both the CEL and the CDF just as for any regular chip type. This are just the first few baby-step thoughts, but it is possible that this chip type could be brought into the Aroma framework with some work. /Henrik On Thu, Nov 12, 2015 at 12:33 AM, Michael Baudis <mbau...@gmail.com> wrote: > 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/. > 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 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. > To unsubscribe from this group and all its topics, send an email to > aroma-affymetrix+unsubscr...@googlegroups.com. > For more options, visit 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. -- -- 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.
