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

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: http://www.ncbi.nlm.nih.gov/pubmed/18573797 Cheers, Mark 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852