[BioC] alternative splicing on human exon array

Mark Robinson mrobinson at wehi.EDU.AU
Tue Nov 25 12:02:49 CET 2008

Hi Dorothy.

Not really answering your SI question here (sorry!), but as a  
variation of splicing analysis on the Affy Exon arrays within R, you  
might try FIRMA in the aroma.affymetrix package.

We would argue FIRMA is an improvement on SI:


On 25/11/2008, at 6:39 AM, dorothyc wrote:

> Hi,
> I'm trying out the alternative splicing commands from the paper,  
> M.J. Okoniewski and C.J. Miller "Comprehensive Analysis of  
> Affymetrix Exon Arrays using BioConductor".  (2008) PLoS 4(2): 1-6.
> I've a couple of questions:
> 1) on page 5, what does "sig.gene" refer to?  I couldn't find it  
> anywhere else in the paper.  I wasn't sure what I'd put there in my  
> case.
> 2) an error would come up when splicing.index(exonmap) is called,  
> saying that the function splicing.index(exonmap) is deprecated and  
> replaced by si().  However, I couldn't find any documentation on it  
> or locate it in BioConductor?!
> Your feedback is very much appreciated.
> Regards,
> Dorothy Cheung
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Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
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