Dear Marcel, I would suggest you try the aroma.affymetrix mailing list which I am cc'ing, because you will get much more assistance there. First of all, the FIRMA results are returned per probeset (i.e. exon) not per gene. I think NA usually is because there is only one probe per probeset (or maybe one probeset per gene too, I don't remember right now). Best, Elizabeth
--- Elizabeth Purdom Assistant Professor Department of Statistics UC, Berkeley 433 Evans Hall (510) 642-6154 (office) (510) 642-7892 (fax) epur...@stat.berkeley.edu On Apr 27, 2011, at 1:27 AM, Marcel Jentsch wrote: > Hi, > > my name is marcel jentsch. I study bioinformatics at the freie > universität berlin. > Actually, I writte my master thesis. In my thesis I've develop a new > alternative splicing detection method and try to benchmark different > existing methods. To do the benchmark I use artifical data. I generate > artificial cel and cdf files. > The benchmark shall also include FIRMA. My problem is that I use FIRMA > in the way it's proposed at the aroma website, but I only get results > for half of the genes. For the other half I get NA. Can you give me a > hint why and how to make FIRMA work? > > Thanks for your help. > > regards, > > marcel jentsch -- 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/
