[BioC] alternative splicing on human exon array

dorothyc dorothyc at bcgsc.ca
Mon Nov 24 20:39:48 CET 2008


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  
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.

Dorothy Cheung

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