[BioC] DEXSeq: Difference in splicing

Dario [guest] guest at bioconductor.org
Thu Sep 27 16:56:15 CEST 2012


I'm using DEXseq to detect differential splicing between two conditions (3 replicates each) and following the guidelines in the vignettes I got a nice table of differentially spliced exons (from DEUresultTable). So far so good.

Now, in differential gene expression you quantify the difference as log fold change between condition A and B. Likewise, I would like to quantify the size of the difference in splicing and the direction. Is this information available from DEXSeq?

Looking at the graph produced by plotDEXSeq() with splicing= TRUE it seems to me that this information could come from the "fitted splicing" (like FC= log2(fittedSplicingB/fittedSplicingA)). 

However I can't find where the fitted splicing data is (I guess somewhere in the ExonCountSet?)

By the way, I found this post https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2011-August/002167.html asking a similar question and Wolfgang mentioned some improvements to the output that could have been addressed in later releses of DEXSeq.

Many thanks!


 -- output of sessionInfo(): 

R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] DEXSeq_1.2.1       Biobase_2.16.0     BiocGenerics_0.2.0

loaded via a namespace (and not attached):
[1] biomaRt_2.12.0 hwriter_1.3    plyr_1.7.1     RCurl_1.91-1   statmod_1.4.15
[6] stringr_0.6.1  tools_2.15.0   XML_3.9-4     

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