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
> universit├Ąt 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.


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