Hi Xinjun. Here is a quick sketch of what I might do.
1. Run everything to get FIRMA scores. See group page for running details and the Purdom Bioinformatics 2008 paper for methodological details. 2a. If Nn or Nc > 1, use 'limma' to look for a difference in FIRMA scores between your two groups. See threads: http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/36d8c59d742fc503/ http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/7d2645bd76cc2023/ 2b. If you have say patient samples (and a good number of them), you might expect only a subset of your C or N patients to have a splicing aberration. In this case, maybe you just want to look for large-in- magnitude FIRMA scores. ... maybe you also want to look at interesting probesets via GenomeGraphs: http://groups.google.com/group/aroma-affymetrix/web/using-the-genomegraphs-package-with-firma Cheers, Mark On 24/04/2009, at 1:01 AM, liszt wrote: > > Hi: > > Now I have N CEL files from both normal and cancer tissue. The two > groups contains Nn and Nc CEL files separately (Nn = Nc). I want to > investigate the difference in gene's splicing pattern between normal > tissue and cancerous tissue. Would you give me some tips? ( I have > read the document and got no answers) Thanks! > > Xinjun > > ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robin...@garvan.org.au e: mrobin...@wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852 ------------------------------ --~--~---------~--~----~------------~-------~--~----~ 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. To post to this group, send email to aroma-affymetrix@googlegroups.com To unsubscribe from this group, send email to aroma-affymetrix-unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/aroma-affymetrix?hl=en -~----------~----~----~----~------~----~------~--~---
