Hi all, I am using the Affymetrix "MOUSEDIVm520650" chip. During the the normalization step for fragment length, the aroma software complains that no probes for enzyme 1 only exist (the same for enzyme 2). I found this discussion: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/880d164e7af6a849/3277e2d8870be696?lnk=gst&q=Mouse+diversity#3277e2d8870be696
In the NetAffx annotation files, all probes have fragment length for both enzymes, although they are sometimes quite large. The affymetrix protocol says that the PCR works well for fragments between 200 and 1100bps. The annotation files for the Genome Wide SNP 6.0 arrays annotate fragments up to 2000bps. To use the aroma software, I want to modify the ufl file and set all fragment length entries < 45 or > 2000 to NA. Unfortunately, I have no plan how to do this. Can someone point me to appropriate documentation? Best, Hans-Ulrich -- 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/
