[BioC] DEXSeq: Difference in splicing

[Alejandro Reyes]

Dear Dario,

Please have a look into the function estimatelog2FoldChanges. With this 
you can get the log (base 2) fold changes!

Best wishes,
Alejandro Reyes
> Hello,
>
> 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!
>
> Dario
>
>   -- output of sessionInfo():
>
> R version 2.15.0 (2012-03-30)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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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>
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