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). 

Elizabeth Purdom
Assistant Professor
Department of Statistics
UC, Berkeley

433 Evans Hall
(510) 642-6154 (office)
(510) 642-7892 (fax)

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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